I've tried using AI to try and solve this issue, but they keep giving me bad information...

In the image below I have an assembly loaded with two parts (a microneedle device and a base I am designing for it).  I want the base to perfectly fit the device and have already arranged my mates so the position is perfect.  

How do I go about intersecting the two models so I can "cut out" the space the microneedle device will occupy from the top of the base it will sit in?  I cannot find any features within the "Assembly" tab that allow me to accomplish this.  

Thank you in advance for your assistance!