How to filter data to remove noise in MATLAB? I have 2 arrays of 800000 input and output data samples. The system is a kind of oven that works from 0 to 10 volts. The sample time is 0.001s.

I have to identify the model of this system, but first of all, given that the data are clearly dirty, I would like to filter the noise.


How can I do it with the System Identification Toolbox of MATLAB?
Moreover, how can I estimate the cutoff frequency to remove the noise?


EDIT:

As suggested, here below are the sampled data plot. As you can see the voltage inputs looks good, but the temperature outputs are affect of noise. I would like to remove it, in order have the output more "smooth".
You can try to remove noise (especially occasional spikes) by non-linear filter. I suggest to use median filter (http://en.wikipedia.org/wiki/Median_filter), as your spikes has length only few points (as I see). There is matlab function - medfilt1. It is probably that such filtration will be enough.