Yeah, probably best to remove the grills in front of or behind the fans dont worry about the grills Pob linked to for the front fans but might be a good idea to have one on the back so that you don't put your finger in it when plugging in cables etc.
For the top fans try some of these to isolate them from the case,
http://www.scan.co.uk/Product.aspx?WebProductId=487037 In fact you can use them on all your fans that attach with screws, the Sharkoon golfballs come with them if I remember correctly.
To do the metal cutting a Dremel really is the best tool but as Pob says don't go out and buy one just for that at ~£50 it makes cutting out a few grills a bit expensive, although I guess you could probably get a cheaper one, something like this available from Maplin
http://www.maplin.co.uk/Module.aspx?ModuleNo=223458 not going to be as good as a Dremel but would get the work done. Oh and remember to wear eye protection (goggles or glasses, will be the best couple of quid you ever spend if it stops you getting a shard of hot metal in the eye!) when using any power tools.