diff --git a/src/Magnum/SceneTools/FlattenMeshHierarchy.cpp b/src/Magnum/SceneTools/FlattenMeshHierarchy.cpp
index f62ecfa3a..9c6edd490 100644
--- a/src/Magnum/SceneTools/FlattenMeshHierarchy.cpp
+++ b/src/Magnum/SceneTools/FlattenMeshHierarchy.cpp
@@ -113,8 +113,6 @@ Containers::Array<Containers::Triple<UnsignedInt, Int, MatrixTypeFor<dimensions,
        absolute transformations to each. The matrix location is abused for
        object mapping, which is subsequently replaced by the absolute object
        transformation for given mesh. */
-    /** @todo skip meshes that aren't part of the hierarchy once we have a
-        BitArray to efficiently mark what's in the hierarchy and what not */
     Containers::Array<Containers::Triple<UnsignedInt, Int, MatrixTypeFor<dimensions, Float>>> out{NoInit, scene.fieldSize(Trade::SceneField::Mesh)};
     const auto matrices = stridedArrayView(out).slice(&decltype(out)::Type::third);
     const auto mapping = Containers::arrayCast<UnsignedInt>(matrices);
diff --git a/src/Magnum/SceneTools/FlattenMeshHierarchy.h b/src/Magnum/SceneTools/FlattenMeshHierarchy.h
index 3ce14cd0c..363150f5d 100644
--- a/src/Magnum/SceneTools/FlattenMeshHierarchy.h
+++ b/src/Magnum/SceneTools/FlattenMeshHierarchy.h
@@ -40,11 +40,11 @@ namespace Magnum { namespace SceneTools {
 @brief Flatten a 2D mesh hierarchy
 @m_since_latest
 
-For all @ref Trade::SceneField::Mesh entries that are a part of a hierarchy
-returns a triple of mesh ID, @ref Trade::SceneField::MeshMaterial and its
-absolute transformation in the scene with @p globalTransformation prepended.
-The @ref Trade::SceneField::Parent field is expected to be contained in the
-scene, having no cycles or duplicates, and the scene is expected to be 2D. If
+For all @ref Trade::SceneField::Mesh entries returns a triple of mesh ID,
+@ref Trade::SceneField::MeshMaterial and its absolute transformation in the
+scene with @p globalTransformation prepended. The
+@ref Trade::SceneField::Parent field is expected to be contained in the scene,
+having no cycles or duplicates, and the scene is expected to be 2D. If
 @ref Trade::SceneField::Mesh is not present or is empty, returns an empty
 array. You can then use @ref MeshTools::transform2D() to apply the
 transformations to actual meshes:
@@ -56,6 +56,11 @@ memory complexity, with @f$ m @f$ being size of the @ref Trade::SceneField::Mesh
 field and @f$ n @f$ being @ref Trade::SceneData::mappingBound(). The function
 calls @ref orderClusterParents() internally.
 
+The returned data are in the same order as the @ref Trade::SceneField::Mesh
+attribute. Meshes attached to objects without a @ref Trade::SceneField::Parent
+or to objects in loose hierarchy subtrees will have their transformation set to
+an unspecified value.
+
 @experimental
 
 @see @ref Trade::SceneData::hasField(), @ref Trade::SceneData::is2D(),
@@ -73,11 +78,11 @@ MAGNUM_SCENETOOLS_EXPORT Containers::Array<Containers::Triple<UnsignedInt, Int,
 @brief Flatten a 3D mesh hierarchy
 @m_since_latest
 
-For all @ref Trade::SceneField::Mesh entries that are a part of a hierarchy
-returns a triple of mesh ID, @ref Trade::SceneField::MeshMaterial and its
-absolute transformation in the scene with @p globalTransformation prepended.
-The @ref Trade::SceneField::Parent field is expected to be contained in the
-scene, having no cycles or duplicates, and the scene is expected to be 3D. If
+For all @ref Trade::SceneField::Mesh entries returns a triple of mesh ID,
+@ref Trade::SceneField::MeshMaterial and its absolute transformation in the
+scene with @p globalTransformation prepended. The
+@ref Trade::SceneField::Parent field is expected to be contained in the scene,
+having no cycles or duplicates, and the scene is expected to be 3D. If
 @ref Trade::SceneField::Mesh is not present or is empty, returns an empty
 array. You can then use @ref MeshTools::transform3D() to apply the
 transformations to actual meshes:
@@ -89,6 +94,11 @@ memory complexity, with @f$ m @f$ being size of the @ref Trade::SceneField::Mesh
 field and @f$ n @f$ being @ref Trade::SceneData::mappingBound(). The function
 calls @ref orderClusterParents() internally.
 
+The returned data are in the same order as the @ref Trade::SceneField::Mesh
+attribute. Meshes attached to objects without a @ref Trade::SceneField::Parent
+or to objects in loose hierarchy subtrees will have their transformation set to
+an unspecified value.
+
 @experimental
 
 @see @ref Trade::SceneData::hasField(), @ref Trade::SceneData::is3D(),
diff --git a/src/Magnum/SceneTools/Test/FlattenMeshHierarchyTest.cpp b/src/Magnum/SceneTools/Test/FlattenMeshHierarchyTest.cpp
index 39240bd9a..d81eb638e 100644
--- a/src/Magnum/SceneTools/Test/FlattenMeshHierarchyTest.cpp
+++ b/src/Magnum/SceneTools/Test/FlattenMeshHierarchyTest.cpp
@@ -52,30 +52,21 @@ struct {
     const char* name;
     Matrix3 globalTransformation2D;
     Matrix4 globalTransformation3D;
-    std::size_t parentsToExclude, transformationsToExclude, meshesToExclude;
+    std::size_t transformationsToExclude, meshesToExclude;
     std::size_t expectedOutputSize;
 } TestData[]{
     {"", {}, {},
-        0, 2, 3,
+        2, 0,
         5},
     {"global transformation",
         Matrix3::scaling(Vector2{0.5f}), Matrix4::scaling(Vector3{0.5f}),
-        0, 2, 3,
+        2, 0,
         5},
     {"transformations not part of the hierarchy", {}, {},
-        0, 0, 3,
+        0, 0,
         5},
-    {"meshes not part of the hierarchy", {}, {},
-        0, 2, 0,
-        5},
-    {"transformations and meshes not part of the hierarchy", {}, {},
-        0, 0, 0,
-        5},
-    {"no parents", {}, {},
-        9, 2, 3,
-        0},
     {"no meshes", {}, {},
-        0, 2, 8,
+        2, 5,
         0},
 };
 
@@ -110,7 +101,7 @@ void FlattenMeshHierarchyTest::test2D() {
             UnsignedShort object;
             UnsignedShort mesh;
             Short meshMaterial;
-        } meshes[8];
+        } meshes[5];
     } data[]{{
         /*
             Cases to test:
@@ -156,11 +147,7 @@ void FlattenMeshHierarchyTest::test2D() {
          {32, Matrix3::translation({1.0f, 0.5f})},
          {17, Matrix3::translation({2.0f, 1.0f})},
         },
-        {{0, 262, 33},
-         {32, 155, 47},
-         {0, 127, -1},
-         /* The above are not part of the hierarchy */
-         {2, 113, 96},
+        {{2, 113, 96},
          {3, 266, 74},
          {4, 525, 33},
          {3, 422, -1},
@@ -172,11 +159,9 @@ void FlattenMeshHierarchyTest::test2D() {
         Trade::SceneFieldData{Trade::SceneField::Camera, Trade::SceneMappingType::UnsignedShort, nullptr, Trade::SceneFieldType::UnsignedInt, nullptr},
         Trade::SceneFieldData{Trade::SceneField::Parent,
             Containers::stridedArrayView(data->parents)
-                .slice(&Data::Parent::object)
-                .exceptSuffix(instanceData.parentsToExclude),
+                .slice(&Data::Parent::object),
             Containers::stridedArrayView(data->parents)
-                .slice(&Data::Parent::parent)
-                .exceptSuffix(instanceData.parentsToExclude)},
+                .slice(&Data::Parent::parent)},
         Trade::SceneFieldData{Trade::SceneField::Transformation,
             Containers::stridedArrayView(data->transforms)
                 .slice(&Data::Transformation::object)
@@ -187,17 +172,17 @@ void FlattenMeshHierarchyTest::test2D() {
         Trade::SceneFieldData{Trade::SceneField::Mesh,
             Containers::stridedArrayView(data->meshes)
                 .slice(&Data::Mesh::object)
-                .exceptPrefix(instanceData.meshesToExclude),
+                .exceptSuffix(instanceData.meshesToExclude),
             Containers::stridedArrayView(data->meshes)
                 .slice(&Data::Mesh::mesh)
-                .exceptPrefix(instanceData.meshesToExclude)},
+                .exceptSuffix(instanceData.meshesToExclude)},
         Trade::SceneFieldData{Trade::SceneField::MeshMaterial,
             Containers::stridedArrayView(data->meshes)
                 .slice(&Data::Mesh::object)
-                .exceptPrefix(instanceData.meshesToExclude),
+                .exceptSuffix(instanceData.meshesToExclude),
             Containers::stridedArrayView(data->meshes)
                 .slice(&Data::Mesh::meshMaterial)
-                .exceptPrefix(instanceData.meshesToExclude)},
+                .exceptSuffix(instanceData.meshesToExclude)},
     }};
 
     Containers::Array<Containers::Triple<UnsignedInt, Int, Matrix3>> out;
@@ -207,8 +192,6 @@ void FlattenMeshHierarchyTest::test2D() {
     else
         out = flattenMeshHierarchy2D(scene);
 
-    CORRADE_EXPECT_FAIL_IF(instanceData.meshesToExclude == 0 || instanceData.parentsToExclude != 0,
-        "Meshes that are not part of the hierarchy are not excluded at the moment.");
     CORRADE_COMPARE_AS(out, (Containers::arrayView<Containers::Triple<UnsignedInt, Int, Matrix3>>({
         {113, 96, instanceData.globalTransformation2D*
                   Matrix3::translation({1.0f, -1.5f})*
@@ -250,7 +233,7 @@ void FlattenMeshHierarchyTest::test3D() {
             UnsignedShort object;
             UnsignedShort mesh;
             Short meshMaterial;
-        } meshes[8];
+        } meshes[5];
     } data[]{{
         /*
             Cases to test:
@@ -296,11 +279,7 @@ void FlattenMeshHierarchyTest::test3D() {
          {32, Matrix4::translation({1.0f, 0.5f, 2.0f})},
          {17, Matrix4::translation({2.0f, 1.0f, 4.0f})},
         },
-        {{0, 262, 33},
-         {32, 155, 47},
-         {0, 127, -1},
-         /* The above are not part of the hierarchy */
-         {2, 113, 96},
+        {{2, 113, 96},
          {3, 266, 74},
          {4, 525, 33},
          {3, 422, -1},
@@ -312,11 +291,9 @@ void FlattenMeshHierarchyTest::test3D() {
         Trade::SceneFieldData{Trade::SceneField::Camera, Trade::SceneMappingType::UnsignedShort, nullptr, Trade::SceneFieldType::UnsignedInt, nullptr},
         Trade::SceneFieldData{Trade::SceneField::Parent,
             Containers::stridedArrayView(data->parents)
-                .slice(&Data::Parent::object)
-                .exceptSuffix(instanceData.parentsToExclude),
+                .slice(&Data::Parent::object),
             Containers::stridedArrayView(data->parents)
-                .slice(&Data::Parent::parent)
-                .exceptSuffix(instanceData.parentsToExclude)},
+                .slice(&Data::Parent::parent)},
         Trade::SceneFieldData{Trade::SceneField::Transformation,
             Containers::stridedArrayView(data->transforms)
                 .slice(&Data::Transformation::object)
@@ -327,17 +304,17 @@ void FlattenMeshHierarchyTest::test3D() {
         Trade::SceneFieldData{Trade::SceneField::Mesh,
             Containers::stridedArrayView(data->meshes)
                 .slice(&Data::Mesh::object)
-                .exceptPrefix(instanceData.meshesToExclude),
+                .exceptSuffix(instanceData.meshesToExclude),
             Containers::stridedArrayView(data->meshes)
                 .slice(&Data::Mesh::mesh)
-                .exceptPrefix(instanceData.meshesToExclude)},
+                .exceptSuffix(instanceData.meshesToExclude)},
         Trade::SceneFieldData{Trade::SceneField::MeshMaterial,
             Containers::stridedArrayView(data->meshes)
                 .slice(&Data::Mesh::object)
-                .exceptPrefix(instanceData.meshesToExclude),
+                .exceptSuffix(instanceData.meshesToExclude),
             Containers::stridedArrayView(data->meshes)
                 .slice(&Data::Mesh::meshMaterial)
-                .exceptPrefix(instanceData.meshesToExclude)},
+                .exceptSuffix(instanceData.meshesToExclude)},
     }};
 
     Containers::Array<Containers::Triple<UnsignedInt, Int, Matrix4>> out;
@@ -347,8 +324,6 @@ void FlattenMeshHierarchyTest::test3D() {
     else
         out = flattenMeshHierarchy3D(scene);
 
-    CORRADE_EXPECT_FAIL_IF(instanceData.meshesToExclude == 0 || instanceData.parentsToExclude != 0,
-        "Meshes that are not part of the hierarchy are not excluded at the moment.");
     CORRADE_COMPARE_AS(out, (Containers::arrayView<Containers::Triple<UnsignedInt, Int, Matrix4>>({
         {113, 96, instanceData.globalTransformation3D*
                   Matrix4::translation({1.0f, -1.5f, 0.5f})*