Sadiah,
as long as your motor doesn't move in a stick-slip manner while determining the TF, dynamic friction should be part of the transfer function of your system. On the other hand dynamic friction is typically not linear and there is a lot of literature available about friction modelling (just search for "friction modelling" in Google or at Amazon...).
Still in most cases you don't have to think about dynamic friction too much as it just damps the system a bit which can be addressed by adjusting the control parameters (e. g. PID).
Static friction is another issue. NI Motion Control boards provide several control parameters to overcome static friction. For the case that you are developing your own motion control algorithm you still may have a look at this
link to get an idea how to address this issue.
I hope that helps,
Jochen Klier
National Instruments Germany