You can clean up images directly at scanning phase by setting and activating the On The Fly operations.   

1. In the input area, activate the On The Fly operations by clicking on the button 
2. Click on the Option menu  (Scan settings) below the Scan button . A window opens.
3. Select your scanner from the drop down list
4. Select one or more image processing operations among:
   • Delete blank pages
   • Auto-rotate pages
   • Deskew pages
   • Remove black borders

5. Be aware however that the more operations you select, the more time the scanning will take.

6. Click on Scan  or press F4

As a result, the scanned images are already processed and cleaned up as per your selection of operations.  

The setting of these operations is saved and the activate/deactivate button gives you the flexibility to use it only when needed.