If the files are not modified after initial creation, you could delete if they have not been modified in over 90 days:
find /path/to/folder ! -type d -mtime +90 -delete
or
find /path/to/folder ! -type d -mtime +90 -exec rm -f {} +
(for versions of find which do not support the -delete action).
 As a matter of safety, you should use a non-destructive version of this command first and ensure it will delete exactly what you want deleted, especially if you intend to automate this action via cron or similar, e.g.:
find /path/to/folder ! -type d -mtime +90 -print
 Note that -mtime +90 checks the modification time of the files and returns true if the age, rounded down to an integer number of days (86400 second units) is strictly greater than 90, so matches on files that have been last-modified 91 days ago or earlier.