You might find it simpler to distill it, or remove it under vacuum, after stripping off the acetone. You can "chase" it with toluene to drive off the last of it.
It will depend of the pKa of your amine. But if you got the acid form (RR'NH2+) yes the NaOH will deprotonate your compound. If you have the RR'NH it depend of the R and R' groups, but generally not.
Find in attach, a paper. They added water to quench the reaction and the solvent was removed in vacuo. The residue was dissolved in DCM, washed with water and saturated brine. The organic layer was separated, dried over sodium sulfate, filtered,
and the solvent was removed in vacuo. Upon purification by silica-gel chromatography using a Biotage Isolute SPE column (eluent: 97∶3, DCM∶MeOH, 0.5% pyridine), the title compound was isolated.