I've basically stripped the whole of the top of my les paul off, and removed the binding. The neck now sticks out a millimetre either side of the fretboard, which I'm going to sand down so it is flush with the fretboard. The frets are also sticking out though, about one to half a millimetre, and I tried going at it with a file, but it didnt seem to take much off.

I'm wondering if there's any better way to remove it, or if I just need to go down each and every one slowly until its flush with the freboard?
You're going to end up with a pretty thin neck, aren't you worried about losing room for bending strings etc?

You can usually go at the frets with a block of wood with some ~200 grit sanding paper, and progress to a file once they're almost flush.
Dremel would do it...but why are you not just re-binding it? You'll also need to change the nut and bridge as the E and e strings would then be too close to the edge of the frets. Curious why you're doing this.
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Agree'd, I'd try re-binding it, the neck would be too small in my opinion.

But if you were 100% you wanted to do this then something like a dremel would do it, much much easier than a manual file.
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The guitar's got a cracked neck, and when it was glued back together by a guitar shop, it never felt the same. So I'm not worried about ruining the guitar, no ones ever gonna want to buy it and it's kind of experience in things for when i make my own guitar from scratch I like thin necks, and as it is at the moment, there's still enough clearance on the high and low e strings for it to be played properly at a later date I may consider changing the nut and bridge though. Cheers for the ideas guys just bought a range of sandpapers so will go at it tomorrow with the thick stuff then the less coarse i'll take some pictures so you guys can see what im doing