Below are some instructions c/p from SCT's site, assuming you have an X4. Other SCT handhelds are pretty similar.
Step 1: Once the device is powered on using the OBDII cable provided, scroll down to highlight “Vehicle Diagnostics”. Press the center button on the X4 keypad to select.
Step 2: Use the up or down arrow button to choose “Read” or “Clear” DTC Codes.
READ DTC: Turn the vehicle key to the ON position and select continue. The device will automatically detect and display any codes that may be present. You will be able to read the definition of the code by scrolling and selecting the code being displayed. To go back to the list of DTC’s, highlight and select the back button.
CLEAR DTC: Turn the vehicle key to the ON position and select “Continue”. The device will display “Clear Codes Complete, Turn Key Off”. Your DTC codes have now been cleared. Select Exit, and Exit again to get back to the Main Menu