Well I guess there's 2 concerns. The first being intake air, the second being exhaust. Many cases do not have top fans, but since yours does the exhaust isn't going to be an issue. So, the intake then. Where does this air come from? Probably, it's going to be right next to a GPU, and GPUs tend to run very hot - 60-90C, depending on the model. CPUs generally should be running below 70C max, so naturally if you're sucking in this hot air that's not a good thing.
So, it really depends on the set up. If your GPU shoots air out the back of the case, then it shouldn't be a bit issue. Otherwise you might consider a couple options. First one is a shroud to help the CPU fan only suck in cooler air/block the GPU air. You could also possibly mount a side fan to either suck out hot GPU air, or blow cool air in - I found that blowing on the GPUs helped them keep cooler temps, but I would assume sucking the air out would overall help the case temps be lower. You could also potentially have the side fan blowing in, but make a shroud to give some pure outside air directly to the CPU fan.