Abstract: Surgical simulators need to simulate deformation and cutting of deformable objects. Adaptive octree mesh based cutting methods embed the deformable objects into octree meshes that are recursively refined near the cutting tool trajectory. Deformation is only applied to the octree meshes; thus the deformation instability problem caused by degenerated elements is avoided. Biological tissues and organs usually contain complex internal structures that are ignored by previous work. In this paper the deformable objects are modeled as voxels connected by links and embedded inside adaptive octree meshes. Links swept by the cutting tool are disconnected and object surface meshes are reconstructed from disconnected links. Two novel methods for embedding triangular meshes as internal structures are proposed. The surface mesh embedding method is applicable to arbitrary triangular meshes, but these meshes have no physical properties. The material sub-region embedding method associates the interiors enclosed by the triangular meshes with physical properties, but requires that these meshes are watertight, and have no self-intersections, and their smallest features are larger than a voxel. Some local features are constructed in a pre-calculation stage to increase simulation performance. Simulation tests show that our methods can cut embedded structures in a way consistent with the cutting of the deformable objects. Cut fragments can also deform correctly along with the deformable objects.