OK lets look at several possibilities; 1 neck bowed too much? Press down the top E string on the 1st fret and on the last fret, look at the amount of space between the string and the frets abuot half way down the neck, a little gap is ok but if there is very much you need to tighten the truss rod, if there is none you need to loosen it. It's that simple and that easy.
2 nut too high? Press string (you have to do each one individualy) on the second fret (actually between 2nd and 3rd) and look at the gap between the string and the first fret, this should be no more than a few thousandths of an inch,notebook paper is about 3/1000 and thats about what you are looking for. If you need to, move the string out of it's slot and useing a needle file carefully file the slot to the desired depth. Do this a little at a time checking the string hight at the first fret often, if you cut it too deep the string will buzz or contact the first fret when played open. Repeat the process for all strings,you may want to have a little more hight toward the bass strings to prevent rattlle.
3 Action too high? correct this by adjusting the hight of the bridge saddles, take them down till the string buzzes just a little then raise them back up untill there is no more buzzing.
4 frets need filed? Yes this can be done but you will need a concave file and a large flat file to do it. First file the frets to the desired hight with the flat file then use the concave file to round the frets slightly. If you leave the top of the frets flat they will buzz.
5 Check and set intonation. Thats the forward/backward movement of the bridge saddles. to do this , tune the guitar then compaire the tones at the octave (12th fret) if the octave note is high adjust the saddle towards the back of the guitar, if the note is low adjust the saddle towards the neck. Do this in small steps and check your tuning frequently. If you plan to use your guitar for recording you should have someone do this useing a strobe tuner.
6 Don't forget the pick ups. After all this other adjusting you will probabaly need to make some small adjustments to your pick ups, this is largely a matter of what sounds best but a good rule of thumb is ... too high, they will distort; too low they wont pick up all they can or should, and allways set the bass side a little lower than the high side.
Do all of this and if you didn't get carried away with the files you should have a guitar that plays as good as it possibly can or you can spend a couple of hundred bucks and have someone else do it for you, either way the end results should be about the same.
Best of luck, Dani