if you have many files in different folders, however they have different names,
assuming they have some common part (“CommonPart”) in the front of their names:

 for i in $(ls Folder1 Folder2 Folder3|grep -oE CommonPart.* |sort |uniq -d) 
 do echo Folder1/CommonPart$i is going to be deleted 
     rm -f Folder1/*$i; 
 done 
 for i in $(ls Folder2 Folder3|grep -oE CommonPart.* |sort |uniq -d) 
 do echo Folder2/CommonPart$i is going to be deleted 
     rm -f Folder2/*$i; 
 done

not very elegant, but effective.