Your description is somewhat vague and leaves me to make some assumptions.
By "motherboard" I assume you mean a PC system board.
By "multimeter" I assume you mean you are measuring resistance.
By "short all over" I assume you mean measuring across VCC and GND in both directions.
Those are all a lot of assumptions to make but any how, here goes.
Finding a dead short across VCC and GND on a complex system board is one of the most difficult repair jobs to perform.
Generally speaking, it can be a short caused by any one of the many ICs but quite often it is a shorting electrolytic decoupling capacitor. It can also be a short between supply lines. I have seen a short caused by excess solder blob underneath an IC chip that crept under heat and gravity after 25 years of operation.
To locate a short between supply lines you will need a current tracer. I am aware of only one that was ever made by HP, the HP 547A (and I am not going to let you have mine).
Without such a current tracer, you have to use the binary search technique where you cut traces on the board and figure out which path the current is taking.
It might be more expedient to get a new motherboard.