One way is to remove the parentheses before splitting. Here I replace all parens with a single space just in case your input ever has adjacent closing/opening parens, like (1 2 3)(4 5 6):

use warnings;
#use strict;

while (<DATA>) {
    chomp;
    tr/()/  /;
    @words = split;
}
$L=($words[2]+$words[5]);
$D=($words[1]+$words[4]);
$M=($words[3]+$words[6]);
print "L=$L D=$D M=$M\n";

# Output: L=37 D=21 M=5

__DATA__
25 ((18 25 4) (3 12 1))
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