Exclude directories from indexing in CLion

Excluding a whole directory isn't possible, however you can exclude files by file type.

Preferences | Editor | File types

Beware that these settings aren't persisted after updating CLion to a newer version (at least this was the case for me when updating from 1.05 to 1.1).

As of CLion 1.5 (EAP for now), you can mark directories as either 'source', 'libraries' or 'excluded'.

See the full blog post describing the new feature:

Although CLion automatically excludes build directories from indexing, some users expect wider options. The same situation can happen when some folders are too big or located on network storage, making their indexing too expensive. To let CLion know that this is the case, you may want to manually exclude folders from indexing.