You do not filter with the state space representation of your filter. You must either use a designfilt (link) object, a transfer function, or preferably a second-order-section representation of your filter. Use the filtfilt (link) function to do the actual filtering.
I sent you some example code on the design and implementation of a Chebyshev Type II filter with your previous post, so I refer you to it and will not repost it here. The only changes you would need to make are to substitute the buttord function for the cheb2ord function, and the butter function for the cheby2 function to design and implement your Butterworth filter. The rest of the code remains the same.
For a general introduction, see Filtering Data With Signal Processing Toolbox Software. There are related discussions available as links on the Digital Filtering page.
