I  sitting here with a system which I have to determine the transfer function. The unit receives a velocity and position, and move towards that position with the given velocity. What kind of test would one perform for determining the transfer function...

I know matlab provides a method. the problem though I am bit confused on what kind of test is should perform, and how i should use Matlab to determining the transfer function. ?

The unit which is being used is a Flir PTU D48E

---> More about the system 

The input for the system is pixel displacement of an object to the center of the frame.. 
The controller i am using now, converts pixel distances to angular distance multiplied with a kp.. which works fine .. but i can't seem to prove why that it works so well.. i mean  I know servo motors cannot be modeled like that.. 

The controller is fed with angular displacement and it position now => added together give me angular position i have to go.. 
The angular displacement is used as the speed it has to move with.. 
since a huge displacement gives a huge velocity.. 

and by updating both element with different freq. i able to step down the velocity such that overshoot gets minimized.. 

The problem here is if I have to prove that the transfer function i found fits the system(plant) PTU I have to test somehow using the IDENT function i Matlab.. and I quite unsure how to do that.. And i am bit unsure on whether the PTU already has a controller within it => since i moves so well.. i mean its just simple math.. so it makes no sense that i can convert it like that..