In the Assembly, click on the one you want to cut and choose the "Edit Part" icon.  That will allow you to edit this Part in the context of the Assembly.

 

 

Now choose the Indent command (Insert > Features > Indent).  Select the Part you want to cut ("Target body:") and the Part you want to cut it with (Tool body region:), and choose "Cut".

 

 

Click on the Okay icon and you're done.