Basic circuit voltage question - Using a driver to control a stepper motor
How do i control the output voltage on the L293D? Do i need to use a
  voltage regulator or level shifter on the output?


You will need to provide 5 volts and 12 volt supplies to the L293D in order to activate 12 volt motors: -



It will operate with 3.3 volt logic inputs but the 5 volt supply should not be lower than 4.5 volts as per the data sheet.

You do not need a level shifter on the output because of the 12 volt feed to the chip. See also this post on some of the problems associated with L293 chips especially when using low voltage motors.