Three way dimmers are available but I suspect you don't have a "dimmer" but a fan speed controller which can not just be replaced with a regular dimmer. Your option if there are no instructions on how to place it on a three way circuit is to wire it up either without the second switch or with the second switch in two way mode (which means both must be on to have the fan run).

You may need to get a wireless remote control system for the fan, and then use the original 3-way switches as another on-off control.

The only trick to using dimmers on a three way is that only one switch can be a dimmer. That is unless you buy the fancy frequency controlled matched pair dimmers. As far as your fan goes, there is no reason that a three way switch would cause the fan or light not to work or the dimmer that came with it. If there is power to the fan from one of the two switches, it should work. Do not however, us a dimmer wired into the three way circuit to operate your fan. It will probably work, but you will usually get a slight hummm.