You want the splice operator.

Incidentally, to get away with removing elements from an array in a for loop, you need to take them in reverse order:

for (reverse 0 .. $#a) {
    splice @a, $_, 1 if condition($a[$_]);
}
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Many of us would write that with grep: @a = grep { ! condition($_) } @a;

You appear to be taking the set differences of two arrays. That has a well-known technique in perl:

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;
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The funny-looking @a{@a} constructions are hash slices.