I am trying to create cylinders within a rectangular box within SolidWorks to model fibers inside a laminate for a unidirectional composite. As a new user, my understanding is that the typical protocol would be to create these (fibers and laminate) in separate part files and combine them in an assembly file (this is done and depicted in the attached pictures). However, I am trying to automate this process, therefore, it not only makes this step harder, but also subsequent steps in the automated process.

When I try to place an extruded cut in the rectangular box (for the laminate) and then fill it again with a cylinder (for the the fibers), the rectangular box becomes whole again and it does not retain the individual cylinders. Is there a way to complete this in one file as to make the automation process easier?

Thanks.