First comment, if you're creating holes, why are you talking about extruding and Booleans? Why not use the Hole feature?
Now whether you're actually using the Hole feature or you're creating a 'Tool Body' that will be subtracted, if you're creating this feature on the seam of two other bodies that you don't want to unite into a single body, what you need to do is perform the Boolean subtract twice, once for each Target body. Now that IS a way to do this with a single Tool Body if you follow this workflow:
Now if you ARE using the Hole feature, when you go to create the Hole, go to the section of the dialog labeled 'Boolean' and set the Boolean to 'None' and place your hole on the seam and hit OK. Now you've got a 'Tool Body'.
Now if you're NOT using the Hole feature but have instead sketched a profile and are going to extrude it to be used as a 'Tool Solid', fine create the Tool Body as a separate body.
Next, using that 'Tool Body' created in either of the previous steps, go to the Boolean -> Subtract function and select one of the two 'Target Bodies', select the 'Tool Body' but before hitting OK/Apply open the section of the dialog labeled 'Settings' and toggle ON the 'Keep Tool' option and now hit Apply. Now select the second 'Target Body', select the same 'Tool Body' over again, only this time toggle OFF the 'Keep Tool' option and then hit OK. Now you have a 'hole' which was subtracted from two different 'Target Bodies' using only a single 'Tool Body'.
John R. Baker, P.E.
Product 'Evangelist'
Product Engineering Software
Siemens PLM Software Inc.
Industry Sector
Cypress, CA
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