I may not be following, but if you're talking about doing jumping in a top down game there are many ways of doing it. One is to handle collision differently while jumping.
Another idea is to store the foot height of your player and a top height of objects. While jumping you would increase and decrease that foot height over time. If the foot height is greater or equal to an objects top height, turn off collision and clamp the foot height to the object's top height while they traverse it.