Try this

@ary1= (1,2,3,4,3);
@ary2= (a,b,c,d,u);

print "Before\n";
print "@ary1","\n";
print "@ary2","\n";

$cnt=0;
foreach (@ary1)
{
push(@new_ary,$cnt), if($_ =~ /3/);
$cnt++
}

splice(@ary1,$_,1,"undef"), for(@new_ary);
splice(@ary2,$_,1,"undef"), for(@new_ary);

@ary1 = grep{!/undef/} @ary1;
@ary2 = grep{!/undef/} @ary2;

print "\nAfter\n";
print "@ary1","\n";
print "@ary2","\n";
[download]

Output:
Before
1 2 3 4 3
a b c d u
After
1 2 4
a b d