I blow any dust that may be on them off with my airbrush. I have a wide mouth jar that I have filled with Future. I trim the clear sprues to a size that allows them to fit into the jar. I dip the parts, shake off the excess and then blot away more with a paper towel. I set the parts someplace dust free to cure. In some cases I will dip them again.
If they are unevenly coated and globby, I stripe them with Windex and repeat the process.
After they have cured for a couple of days I will start the masking process. It is important to understand your construction sequence before painting. You may have to undo a whole lot of work if you paint too soon. Getting the canopy to fit and flush mount might require some sanding and filling, so you need to have those contact surfaces free of paint and Future.
Here is a windscreen that didn't meet muster it needs some filler to eliminate the lip/gap.
Again another one (but this build did not use any fillers in the process) but if it were to be a finished model, this canopy issue would stand out like a thumb just struck with a hammer.
Mastering canopies, windshield, blisters is an art in itself. Get that licked and the rest is gravy in comparision. An otherwise perfect model can be out of the running due to the installation quality of the clear parts. Some require vast amounts of fiddling.
Applying Future is a great insurance against any scratching during assembly. If something goes a muck while assembly, it can be removed and reapplied while the canopy is attached. But as long as you have the glass parts masked you should have any problems.
Oh, I mainly use solvents to attach my windscreens, I rarely ever use CA on clear parts, but if you do Future is a must to keep the clear parts from fogging.