I assume that by CNV you mean a sequence of DNA that is present in 2 copies in some subjects and in 1 or 0 copies in other (i.e. a deletion). If by CNV you mean a portion of DNA that is present in multiple copies then the situation is more complex. This said, you might design a primer pair on the border of the CNV and confirm it either via PCR + gel, or by sequencing the breakpoint (Sanger would suffice). See the picture I created for guidance: basically, you have to design two primer pairs. If the 3 exon region is present in both alleles you will be able to amplify couple 1F-1R and 2F-2R but not 1F-2R. If your 3 exon region is heterozygous then you will be able to amplify all the three pairs. Finally, if you have an homozygous deletion you will only be able to amplify the pair 1F-2R.