Due to the fact that you are mentioning the $A,B,C,D$ matrices I assume that your model is a linear one of the form:
$$ \dot{x} = Ax + Bu$$
$$ y = Cx + Du $$
where $x$ is the state vector and $y$ the output of the system. One thing you can do, at least I would go like this, is transform your system to the $\text{s-domain}$, that is obtain the input to output transfer function:
$$ T(s) = \frac{U(s)}{Y(s)} $$
Since you can measure both the input and the output of the system, collect some data by stimulating the system with some input signal and measure the output. Store both input and output data to vectors. The input signal though should not be some random arbitrary signal. It should be a collection of step inputs, a pulse signal, a summation of sinusoids or even better a random sequence such as (pseudorandom binary sequence or gaussian white noise). The sum of sinusoids can excite a finite number of frequencies, particularly the signal:
$$ u = \sum_{i=1}^m A_i\sin(ω_it) $$
is called sufficiently rich of order $n$ ($n$ is the number of the system's unknown parameters) if and only if $m \geq \frac{n}{2}$. So, in order to excite all the necessary frequencies of your system you need to know how many unknown parameters you need to estimate. On the other hand, random sequences as the ones I referred to previously, can indeed excite all the frequencies and could be a really good option in order to obtain input-output data which contain all the information needed to perform a really good system identification. I really encourage you to take a look at the Robust Adaptive Control book, which is available online. It really deals with those issues in a great in-depth way.
Now, you have the equation of the transfer function (it should be a third order) and a collection of input and output data. You got everything you need in order to proceed and perform the identification of the unknown parameters of the system.
I find it easier to use the System Identification Toolbox in order to estimate transfer function models. When estimating transfer function models you only need to specifically set the input and output of the system. Of course do not forget the very important step of processing your data. You may have to attenuate any possible noise, choose which part of the data you would like to use (because you have a linear system it would be best to work with output data that present a linear behavior with respect to the input data), normalize them or a whole bunch of them. Of course the toolbox can do these stuff for you by selecting the appropriate choices.
To conclude, you have now obtained a transfer function model of your system. You can easily convert it into a state-space representation and apply any state feedback control law you want.