The pins go inside the microcontroller where they have ESD protection diodes to the power supply. That means applying a higher voltage (Supply+0.5 is about max) can damage it. There is also ESD diodes to ground which means the pin must not go much below ground.
If you supply 3.3V to the microcontroller then it needs to run slower, Sparkfun has this one for example.
But anything timing related turns into a job.