CrystalMaker makes it easy for you to show or hide groups of atoms, either by direct selection (select a group of atoms, then choose the Selection > Hide > Selection command), or via the Site Browser (to make this visible, choose: Window > Sidebar > Site Browser).

If you wish to hide all atoms of a particular kind (e.g., all hydrogen atoms in an organic structure), simply locate the relevant element row in the Site Browser (this is the row with a disclosure triangle and an element symbol), then uncheck the Vis checkbox. All sites with that element symbol will now be hidden.

You can also use the Site Browser to hide all atoms that reside on a particular crystallographic site (e.g., the "T1" site in a feldspar mineral): this time, locate the relevant site row (you may need to open up some element rows to find the site row) and uncheck the site's Vis checkbox.