It would help to have the data, and a description of the desired result, since I do not understand ‘background continuum emmission’ or what it does to the signal.
One option could be to use the islocalmin function with the appropriate 'MinProminence' value, fit that result using polyfit (and polyval), and then subtract that from the original signal to ptroduce a more consistent baseline. That approach has worked in other applications for me.
