Yeah... definitely more a technique issue. The recording process is far less forgiving than practicing/gigging. Every little flaw comes out. The good news is it will make you a better player. Keep practicing into the DAW paying attention to every movement you make. Warming up with some scales and position changing exercises beforehand is advisable. Also some guitars can make the little imperfections stand out more so if you have other axes around give them a try or rent/borrow something. A lot of dudes will keep guitars around specifically for recording (I bought my Yammie because I didn't trust my other guitars although they were good live).

As far as effects someone mentioned R-Mix. It is really good for doing precise surgery on stuff like this. Just watch the R-Mix window when you hear those squeaks and squawks then isolate where the little blobs show up when it's happening. You don't even have to turn that area down all the way. Just enough to keep it from overpowering the rest of the signal. Also if you are using a sim like TH2 or GR make use of the global gate features. May not do much in the middle of a performance but it can help tame things a little. Compression can help smooth things out a bit better too.

Just some extra things for you to try. Obviously checking out different options to see what works for you is best.

Cheers.

Frostysnake


@ Marcus Curtis - I have never heard of this...my hbody chemistrydestroys a set of strings in a day if I don't wipe them off...wonder if this might help...LOL

Sometimes the tops of the fingers get rough and jagged and that winds up being the thing that causes noise and squeaks. Other times it is a skill level, either way this solution should take care of it. It works for me. Sometimes I have this problem with really hard acoustic pieces. It worked for other members of the guitar society that I recorded too. 

I always have a bunch of emery board lying around anyway to shape the nails on my right hand anyway. I got the idea and tried it. I was amazed at how well it worked


Only sand enough to smooth things out you don't want to sand off a layer of skin. a very light and refined sanding should do it. 

Ok...so leave the callouses on, right?

Frostysnake


Ok...so leave the callouses on, right?

right....don't mess those up your gonna need them.

Try coated strings. 

I'm half agreeing with Mike McCue, because if you don't want to try flat wound you could try half flat.  I started using these a year ago.  They took a little getting used to and aren't as bright as round wounds, but I've come to like them:
http://www.daddario.com/D...ID=3768&familyid=2

That said, as many here pointed out, recording has really forced me to clean up my playing in general.  I'm pretty adventurous about trying to fix things using Sonar but I've consistently found that I get better results if I just learn how to play cleaner... with the occasional punch-in.   Actually, I heard Joe Walsh had a similar experience when he started recording.