Is there a way to delete the unused category in cognos transformer .
Thanks,
Highlight the item in the Categories diagram and hit the delete key.
If you mean saved categories clean house from the tools menu. You can specify the date that they have not been used since. If you mean suppression of some sort there are options for the level as well as individual categories in the category diagram.
Clean house has risks, mainly related to the now missing category still being present in report filters, category views (often used for security), etc. Also, it will wipe any calculated or 'special' categories, e.g. a Cognos-generated time dimension.
If you want to use it, I would back up your existing cube model and be sure to test it out thoroughly first, including at the least the more important reports.