Been some time since I played so bear with me. Easy method: get stealth vehicle with cloak
and CAREFULLY drive it to manframe. Instruction book should tell command for targeting
items in crosshairs, but I think it's the TAB key. Hard method: eliminate all anti air
capability for enemy, and send a Pegasus to pick up mainframe via the tactical map screen.
If you press the number key for the Pegasus twice, but do not take over the controls, then
the soulchip ***igned to pilot it should pick it up and lock on. If not, you might need to
manually target the mainframe using the Pegasus yourself.

Addendum to last: TAB targets nearest under reticle, M targets nearest mission critical.