System Identification in a closed-loop feedback system
Closed loop:
$$H(s) =\dfrac{F(s)}{1+F(s)}$$
where F(s) is function of the open loop system. Now if you have a controller C(s) in series with the system this becomes:
$$H(s) =\dfrac{F(s)\cdot C(s)}{1+F(s)\cdot C(s)}$$

You have to solve F(s) from known C(s) and H(s).