My basement has a rough in for a shower. We will not be installing a shower. How do I cap it so I can install my subfloor over it

What material is the drain made of? Metal (copper or cast Iron) or plastic?

Plastic

Either cap it off or put in a plug. You may have to chip away some concrete to get a cap or plug flush with the floor. If necessary, use a forsner bit to relieve the subfloor over the covering. Make sure that you cement it in/on well.