Controlling Certain Solids Under a Surface?

First of all Hi. I am new user for grasshoper I can say. I have created a organism thas has both seating and shelter part. However, now. I want to control the boxes under the surface that I have created. Is there a way that I can pick these solids or should I create whole thing from the start? Thank you for your attention… (And also I have one more question, I dont understand what is the reason one of the cylinder is always short when the others are perfectly true. Thank you for help again.
parametrik.3dm (2.4 MB) (43.9 KB)