Hi Zuhaib
You can import directly and perform 3D classification. You only need to re-extract if you want to recenter the particles, or if the particles you fed into cryosparc were binned.
If you already have some density for the region of interest, and you just want to sort which particles have that density and which do not, you may want to perform a 3D classification skipping alignments, with a mask around the region of interest and a decent number of classes (~8-12). Just remember if you do this, you’ll want to increase the regularization parameter T - I often find 100-400 is a good range in such a case.
Cheers
Oli