I have a RHEEM furnace with a hot surface ignitor. The flame sensor will only register .01 microamps, not enough to keep the burners fired. What is the procedure for checking polarity for the furnace, and what could other possible causes be? The flame sensor is new, and the gas pressure is 3.5 inches WC.

You checked it on DC mA, correct?

Polarity is just making sure the ground to neutral voltage to the furnace is near zero and not 120 VAC. The furnace must be grounded correctly too.
If the ground is bad, then no go.

Troubleshooting techniques:

Troubleshooting a flame rectification system - Feature Articles - Extra Edition - Air Conditioning, Heating & Refrigeration NEWS

I guess the only other possibility is the furnace control board.