As count mike said, exhaust does not need filters. This is why a dust filter does not come with the fan at the rear of cases.
As far as air flow, putting the rad on top is perfectly fine. You may actually get a little better airflow because some cases restrict air from the front due to the front cover.
But going on top has its draw backs as well, if you have an open air GPU, then the hot air from the GPU will be pushed up through the rad. So you will be using hot air to cool the CPU.
But in the end, front or top, there will only be a degree or two difference either way you go.