If a node is selected to be deleted, in the FEM, and the following error message displayed message is: embedded object cannot be deleted in isolation, the following scenario may be the reason.
Often, nodes cannot be deleted if they are attached to elements, loads or constraints. However, they can be attached to other objects that will also prevent that node from being deleted. Sometimes it may be more difficult the find the associated object. In this example, listing the node to be deleted did not list any connected elements. The idealized and Master Part were not active in the FEM so they were loaded. Once the CAD geometry was loaded, the node could be deleted. It turned out that the node had been associated to a polygon edge by a 1D connection and the CAD geometry had to be loaded before the node could be deleted.