I just got a Helix LT, and ran into this issue with one of my guitars, which caused me to look here. I have a mix of the usual Fenders and Gibsons, and was pretty happy with the sounds I was getting until I plugged in my Fender Lead III, and I hear this horrible pop-pop pick attack noise. I mean really obnoxious. I knew it wasn't my pick or technique, because my other guitars all sound just fine with no pick pops. A fast-attack compressor as suggested above sounded like a good idea, but it didn't do the trick - the pops were quieter, but definitely still there. I fooled with the amp tone settings and the Helix global EQ, but getting rid of the pop required killing way too much of the good stuff. Which told me maybe I needed to deal with the issue earlier in the signal chain.
I noticed that by turning down the volume knob of the guitar down to 6-7, I was able to get an acceptable pop-free signal, which clued me that maybe the guitar output was simply too high or too bright. The guitar tone control didn't help nearly as much, and had other side effects. But, I found that by inserting a Low-High Cut EQ as the first block in my signal chain, I was able to effectively get rid of the pops before they were picked up by my downstream effects. What worked best with my Lead III was a high-cut at 9kHz and -10db on the level. I can now turn the guitar volume pot to 10 with no pops. It does reduce the signal volume, but that's easy to deal with in other ways downstream that don't color the tone.
