Yes, you can hide (or edit) groups of spells, as well as just one spell at a time.

In the Spell Timer and Cooldown Timer this is both done in the 'Coloring/Filtering' options category.

To hide a group of spells: simply uncheck the checkbox belonging to the group.

To hide just one spell: go to the option under 'Coloring/Filtering' called 'Customize'. Here you can type in the name of the spell you want to hide (or change). Once you have put in the correct name you can use the dropdown next to the name input to set it to 'hide'. It's also a good idea to select the proper type of your spell instead of 'all'; this will avoid unneeded problems. (Hint: Right-clicking an icon on the bars will also fill in the right spell type for you)