findpeaks in the Signal Processing TB can be very helpful for such -- remember a minimum is the maximum of a negated signal.
Per usual, if you were to expect any really specific input, attach a sample of the data...and, if you can plot the data, you can operate on the data used to make the plot instead of extracting it back out of the figure.
If you're manually selecting the points w/ ginput or the like; there's sample code to save those in a variable from the callback function; once you have that array, outputting it to a file is trivial.
Again, too little info for specifics...
