Thank you, it seems that the cylinder did extend down through the whole model and as soon as I changed that so that it stopped when it got to the top of each step it managed to fix it.
(I do apologize i should have specified what modeling software i was using but the solution that i was given worked anyways)...(I was using Rhino 6)
As seen by the dotted red line, i used the edges of the steps to trim the cylinder.
Thank you for the help, I was stuck with this for a while, I just wanted to post the process of my solution if any other people have the same problem.