Removing Interior Boundaries
Removing interior boundaries is good practice if the interior boundary is an effect of the geometry modeling and does not represent a border between different materials or between domains with different properties. When you remove the interior boundaries, the resulting geometry consists of fewer domains and puts fewer constraints on the mesh generation.
To remove interior boundaries, clear the Keep interior boundaries check box in a Boolean operations such as Union or Compose.
It is sometimes useful to keep interior boundaries for controlling the mesh. In such cases, use virtual operations such as Ignore Edges and Ignore Faces but keep the original interior boundaries for mesh control. The interior boundaries are then not part of the geometry for defining physics nodes but are present during meshing to define areas where you want to use a finer mesh, for example. See Controlling the Mesh Size Using Mesh Control Entities for more information.