system identification procedure

Have Simulink data available in MATLAB workspace as double vectors. In the GUI (ident) import time signals to load the data. Then you work from there. If you are estimating models in the command line, package the data into an iddata object:

 data = iddata(y,u,Ts); % y = output; u = input; Ts = sample time

Then try various estimation commands, e.g:

 model = tfest(data, 2); % second order transfer function

The logged data (y,u) must be equi-sampled. If not, interpolate them to a uniform time grid.