Some possibly helpful guesses etc...
Does the amp sound scratchy when you're recording it? If not, you might want to try putting the mic in a different spot. If you're putting it flush with the amp grille pointing in at the center of the speaker cone, you'll get a scratchy treble-heavy sound. Gbondo's idea should help.
If it DOES sound scratchy during recording, then the amp/amp settings/tone setting/guitar cord/guitar itself is/are the problem(s).
You may also be using too much distortion. Too much distortion can lead to a thin, scratchy track. You could try using two tracks recorded separately with less distortion. This applies even if you use a modeler like a POD or a J-Station rather than a miced amp.
The line out on your amp-- is it emulated? A straight line out that doesn't have cab modeling will usually not sound very good when recorded.
I finally got a recorded guitar sound I liked by layering a few different tracks (3 in fact), each with a different distortion/patch, in each channel. One track is a thick punchy boomy Mesa Boogie emulation, another is a thinner midrangey old Vox emulation, and the third was a Boss Metal Zone pedal run into a puny junky Crate practice amp and miced with a 57 (off center, angled for the windscreen top to be more or less parallel with the speaker cone) which added some mids and the crunchy crispy high end, as well as added some "realism" to the emulated tracks (emulated sounds sometimes have this "fake" sound... ferinstance my emulator, a Zoom, lacks some high end). Soloing each track, they sound pretty lousy (except maybe the Boogie sound
), but each added some essential part to the wall of distortion they created together. I was kinda surprised at how well it worked.... of course if you have a nice amp (or better yet TWO nice amps for the different characters) it may work even better. For me though, I'd rather avoid using my amp.