You can delete custom reports you've made in the past as they become obsolete to your business needs.
To delete a custom report, go to the Reports tab, then click on either Employee Report Builder or Pay Report Builder; wherever you created the custom report initially. Next, click on Open Report and select the report you'd like to delete from the drop down list, then click Load.  You will now see there is a Delete Report option at the top right of the screen, click this and then click Yes to delete the custom report.