Remove Punch Holes (This function may or may not be available depending on the scanner model you purchase.)  
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Tick the check box of Remove Punch Holes, the hole marks aligned along with the edge of the scanned document will be removed after auto crop is done. The function will work for the document with single background color.  
 
GB_TWAIN_Preference_Remove punch holes  
 
Color of the Background Paper  
If you select this option, punch hole marks will be filled with the background color of the scanned document.  
 
Custom  
If you select this option, punch hole marks will be filled with the selected color.  
 
When you scan by the Color Mode, clicking button ... button would allow you to choose the desired color to remove the punch hole marks.  

When you scan by the Grayscale Mode, clicking button ... button would allow you to choose the desired color to remove the punch hole marks.  

When you scan by the B/W Mode, punch hole marks will be filled with white color if you click edge fill button-1 button, or punch hole marks will be filled with black color if you click edge fill button-2 button.