What kind of measurement equipment do you have?
A GSG probe and S-parameter measurement equipment are
certainly capable of pretty low value capacitance readings,
especially if you have an opens and shorts de-embed pair
on the same die.
You might also want to make arrays of unit MIM caps and
do the math, rather than try to measure just one. That
will help bury the interconnect capacitance somewhat.
Don't blame the pads for inability to measure; put down
a duplicate structure, delete the MIM cap, take two
readings and do the math. You also don't have to use
approved pad structures with all their baggage; a passivation
cut and top metal only makes a perfectly good probe pad.
If this is a test chip and not something that needs to
pass some pile of corporate a$$-covering can't-do rules,
anyway.