Click the TOGGLE FILTERS link on the top left of the reports screen to show the filter side bar.
In the filter side bar just select the items you need to filter on. Most items use check-boxes but some will be just plain text where you enter a search string (such as custom fields that are defined as free-form text fields).
Click the RUN REPORT button ( Note: This used to be the APPLY FILTERS button in prior versions)
Filtering With Custom Fields
If you created custom fields of your own and need to filter on those fields you first need to enable them for use in reports. To do this go to TICKETS->REPORT SETTINGS. There you will see a list of custom fields used in the system. Just check the ones you want to use in reports and click the SAVE CHANGES button.
Warning: Only enable the custom fields you absolutely need! Some fields will let you return nonsensical results in your reports so be careful and only enable the fields you really need and understand!