Hmm. Shouldn't be too difficult. If the guns are held in hand, then just chop them off with your clippers and treat the model like any other. If they are held up against the chest, it becomes a bit more of a pain.
I use (again) the clippers to cut away as much of the gun as possible (you just want your new gun to fit in) and then file down any rough edges. Use greenstuff to patch up/smooth over any scarring in the metal, since it requires you to be a bit more rough when working with metal.
If you have sprue clippers (
like these) then they should be able to cut model-metal. (Don't try anything harder than that, though!) Mine have never had a problem with it. A jeweler's saw works wonders for larger cuts. Your hobby knife will be able to handle many of the cuts you will need to make as well (like, say, through a wrist or an arm) and can easily slice off small bits like insignias. For raised things that need removal, especially ones that aren't in a recess, a file will be the best way to remove the offending gubbin without risking damage to the model. Depending on what area of modelling you feel comfortable with (filing, cutting, greenstuffing) you will find a preference for how you handle your metal minis.
Personally, I hate greenstuffing, so I try to avoid having to do it at all costs. When I removed the Ultramarines symbol from Telion's shoulder, I spent an hour or so filing it down gradually, rather than hack it off and have to patch the shoulder with greenstuff.
Since metal models don't fuse together when you glue them (like plastic bits do with plastic glue) I cannot recommend pinning highly enough. When it comes to metal or resin models, I prefer to pin every last joint.
In any event, I hope all that helped. If you have any questions, don't hesitate to
PM me! I may not be the world's best painter, but I think I do some pretty sweet conversions, so I'm more than happy to try and offer any help I can.