WP-Filebase search integrates with Relevanssi. There are a few things you need to do:

• In WP-Filebase settings / File Pages enable “Content Keywords”
• In Relevanssi settings make sure to enable indexing for “wpfb_filepage” post type
• After changing the settings run a rescan (WP-Filebase Dashboard / Tools)
• For searches inside documents use Document indexing extension