App Cleaner scans all applications installed on your Mac and then lists them in the left-hand column. However, you can exclude needed apps from being scanned with App Cleaner by changing the scanning options in the app’s Preferences.
1. Go to Menu → Preferences → Skip List tab.
2. Click the + sign in the bottom left-hand corner to add all needed applications to the Skip list.
The next time you run App Cleaner, programs on the Skip List will be excluded and will not be scanned.