Processing of distorted guitar samples
Much has been said about recording so I presume you have the samples stored in one file, normalized to 100%, noise is removed and each note has 2 picks (the first one that is going to be cut off and the second which profits from that).
Picks are the biggest problem of miced guitars. As you can see on the picture, there's a large kick drum-like wave between start of the second pick and clean guitar sound. It's usually not as plain as on the picture below. The unwanted bassy part looks always fat compared to the rest and can't be missed but it's borders are often hard to locate. In some unlucky cases the beginning of the pick is too short and the fat thing split in two or more separated parts. Finding the right borders and making reasonably sounding cuts is difficult and you have to experiment more than you'd like to.
This picture shows reasonable borders.
Once you cut the fat pick off, there'll be most likely a sharp difference in amplitude that has to be corrected eiter manually or automatically with some wave cleanup utility (much better results).
Once the bassy artifact was successfully eliminated, you shape the pick as you want. Cut is not always the best way how to lower the presence of a pick. Some volume envelope or 70-100% volume fade may do it better in case the pick is dangerously short already.
Another problem is resonances that occur during the note fadeoff and cause large changes in volume. In the following case, VU meter shows -6db at the beginning and -0.6 at the end. This has to be corrected with a compressor.
Set the compressor threshold to the target level (-6db in this case) and compression rate to more than 10:1. Attack and release settings are not much important in this case, att: 5ms and rel: 100 should work.
This picture shows a reasonable result.