I'm assuming that you are using a .wav file. First you will want to use wavread to read the audio data into Matlab. Then you could use logical indexing, like audio_data(audio_data > thresh) = max_value; in order to force values above a certain value.
You could also find peaks by finding where the derivative is 0 (use the second derivative to find if that value is a min or a max), and set the local maxima to your predetermined value.
Hope this helps!