I would recommend that you take a look at the signal in the frequency domain, and try to figure out whether the noise is primarily at frequencies that are lower or higher than the signal of interest. Also, is the signal of interest limited to a certain frequency range or band.
Based on this information, you may be able to design an appropriate filter (or sequence of filters) to reduce the noise while retaining the signal of interest.
The easiest way to design a filter initially is to use the Filter Design and Analysis tool or fdatool. For more information: