Convert Custom Table Data Based Plugin To Be Searchable

There is the post type attachment, which is normally used to store information about files uploaded to WordPress’ Media Library. Additional data can be saved into custom fields/postmeta. You definitely should look into that, if you decide to go with native WP tables.

Another possibility would be to make those custom tables searchable, on the codex page »Custom Queries« you find an example about »Keyword Search in Plugin Table« which should get you started.