There are multiple ways to do it. If you want don't want the variant to show on the POS, you can add that item into assortment as an excluded line.
If you want to avoid users from doing purchase, sales or inventory transactions on the specific variants, you can try enabling the stopped flagged under the default order settings that is available under Released Products >> Manage Inventory. MS recently added a functionality to make the assortment respect the stop flag while exploding the lines.
If this helped you, I'd appreciate it if you'd mark this as a Verified Answer, which may in turn help others as well.
