diff --git a/src/bonsai/bonsai/bim/module/root/operator.py b/src/bonsai/bonsai/bim/module/root/operator.py
index 5ad4aeae3e..636a3635ce 100644
--- a/src/bonsai/bonsai/bim/module/root/operator.py
+++ b/src/bonsai/bonsai/bim/module/root/operator.py
@@ -199,6 +199,16 @@ class AssignClass(bpy.types.Operator, tool.Ifc.Operator):
             if obj.mode != "OBJECT":
                 self.report({"ERROR"}, "Object must be in OBJECT mode to assign class")
                 continue
+
+            # Clear any transform modifications.
+            if not tool.Blender.apply_transform_as_local(obj):
+                self.report(
+                    {"ERROR"},
+                    f"Object '{obj.name}' has parent/constraints with a shear transform that cannot be applied safely as a local transform. "
+                    "Please apply parent/constraints manually and try again.",
+                )
+                continue
+
             element = core.assign_class(
                 tool.Ifc,
                 tool.Collector,
diff --git a/src/bonsai/bonsai/tool/blender.py b/src/bonsai/bonsai/tool/blender.py
index 97d188a321..539b7664fa 100644
--- a/src/bonsai/bonsai/tool/blender.py
+++ b/src/bonsai/bonsai/tool/blender.py
@@ -1233,3 +1233,27 @@ class Blender(bonsai.core.tool.Blender):
         system = bpy.context.preferences.system
         system_scale = system.dpi * system.pixel_size
         return (system_scale / default_scale) * size
+
+    @classmethod
+    def apply_transform_as_local(cls, obj: bpy.types.Object) -> bool:
+        """Apply object transforms as local matrix, if possible.
+
+        Clear parent and constraints.
+
+        :return: `True` if transform was applied and `False`
+            if transform wasn't applied it's not possible due to a shear.
+        """
+
+        if not obj.parent or not obj.constraints:
+            return True
+
+        matrix = obj.matrix_world.copy()
+        # Matrix has a shear, it cannot be represented as a local matrix
+        # based on rotation+translation+scale.
+        if not matrix.to_3x3().is_orthogonal_axis_vectors:
+            return False
+
+        obj.parent = None
+        obj.constraints.clear()
+        obj.matrix_world = matrix
+        return True