: He forces Father's snot into the Code Module. This tricks the device into identifying Father as a KND operative, causing the ray to backfire and transform Father into a tiny animal.
: He removes his own DNA (specifically his booger) from the Code Module, making him immune to the ray because the device no longer recognizes him as a KND operative. [S3E10] Operation G.R.A.D.U.A.T.E.S.
In the Codename: Kids Next Door episode (which is actually Season 3, Episode 9 ), the "helpful feature" refers to a logical weakness Tommy Gilligan discovers in Father's Animalization Ray . : He forces Father's snot into the Code Module
Watch how the ray's specific targeting mechanism leads to Father's downfall in this episode recap: Episode 9 )