for (reverse 0 .. $#a) {
    splice @a, $_, 1 if condition($a[$_]);
}

##</code><code>##

@a = grep { ! condition($_) } @a;


##</code><code>##

my (%a, %b);
@a{@a} = ();
@b{@b} = ();
delete @a{@b};
delete @b{@a};
@a = keys %a;
@b = keys %b;
# or if order matters,
# @a = grep {exists $a{$_}} @a;
# @b = grep {exists $b{$_}} @b;