I have an old Framus Superstrato that doesn't produce the correct notes at about 5 of the lower frets (from about the 15th fret to the 20th). It instead produces the note that the 21st fret would for each of those frets. I think it is because my neck is not particularly straight at the lower end. I took my guitar in to guitar center to get some input and he said that it wasn't the truss-rod that was causing the issue.

So I was wondering if it would be bad if i were to unfret the lower neck and sand the fretboard until it's straight.

I don't want to raise my action because it's really not too enjoyable to play like that.
From what I've heard GC aren't very reliable in the repairs department.

What I'd do is this:

Google truss rod adjustment and learn.
Google fret levelling and see if this fits your problem.
If you can't I.D your problem through this, visit your local luthier/repairshop and ask their advice
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Most GC "techs" are horrible and know next to nothing. Find a decent small music store and ask them if they do luthier work or if they know of a good luthier in your area.

Where are you located? maybe someone here knows of a good luthier in your area.

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This... Seriously most GC workers I have spoken to know absolutely nothing about guitars. I pointed out how a squier strat had sharp fret ends and they said well most squiers are going to have that. I also have seen a guy bring in a guitar for a setup and get told that they couldnt setup his guitar because there wasnt a truss rod. It had the truss rod adjustment at the neck heel. Then I heard a employee who thought he was just the best thing to walk the earth complain that he was getting rid of a guitar because of a cracked headstock that he believed wasnt fixable but it wasnt even broken fully, just cracked near a tuner. GC workers more often than not tend to be total morons who honestly should not be allowed to touch a guitar. If I want to find someone who actually knows anything about guitars I go to mom&pop style guitar shops.

Find a local shop thats not a GC and have them check it out, im betting that the fretboard doesnt need to be modified, probably just some adjustments to the neck, maybe a shim, or fretwork done if not a combination of these.
thanks for the responses. I guess I could try looking around more before taking matter to my own hands. I just assumed that the luthier at GC wouldn't say my guitar is doomed (which is basically what he said) and would instead help me fix it. He said I need a new neck which I hope isn't true because I do like my current neck and it would be very difficult to find a matching neck for this particular guitar.

I sometimes see ads on craigslist for guitar repair so I might try one that looks reasonable and knows what he's doing. In the meantime, I guess I won't be able to play down the neck too much.
First thing I would look at is if your 21st fret is raised up any.

Does it look like there is any space between the bottom of the fret and the fretboard?
Compare that to how the other frets look.
Tapping it down with a little plastic hammer may be all you need to do to it if so.
Last edited by CodeMonk at Apr 5, 2014,
Only if you think the fret board some how became something other than flat & level.

If the neck is warped it probably needs replacing.
If frets are not level, easy fix.

But to the original symptom. If I understand you, it is not intonating properly which is another beast altogether. That involves moving the saddles of the bridge to lengthen or shorten the strings.