I used a large baster to separate the naptha, that turned out to be a bad idea since it is so large you can't get it all out without getting a little of the purple stuff.

I removed most of it, but there are still some tiny grains with the crystals (I'm using the freezing method).

what do I do?

you could get a pipette or a separatory funnel.

you may just have to leave some of the naptha behind in the container until the next pull. I would say it is more important to leave the soup behind than to get all the naptha.

did you do a straight to base method with mhrb or an acid/base with acrb?

Before putting the naphtha into the crystallisation vessel, put it into an intermediary container such that the basic sludge residue can be separated from the naphtha nice and easily.

(Cosmic goats, this statement needs to be a standard bumped message so I don't have to type it out every other week... )

Okay I will use the coffee filter. But what do I do now that the DMT has been crystallized?

I would advise against using a coffee filter at this stage. Your best option would be to warm up your solvent and redissolve the contaminated crystals. After everything is nicely dissolved, work on separating the basic plant mix from the non polar solvent. Filtering through a glass or stainless funnel stuffed with cotton at the end could also help to ensure the solution is filtered properly. I would also advise doing at least one re-crystalisation. A basic water wash on the other hand would definitely be the best approach in these situations, but it's best to stick with the simpler methods of cleaning if you're not yet aware of such procedures. Good luck!