i have a 2001 4 runner,

question is how to remove spare tire under the car, manual
says there is a nut to turn and lower the tire,
yet the actual spot i do not see.

what gives ?

If you open the rear hatch, there is a hole that accesses the screw above the spare. The jack handle slides in this hole and engages the screw. When the jack handle is turned, the tire lowers. The hole guides the jack handle onto the screw.