How large an array does one of these files create in memory? The size of a .csv file is extremely dependent upon how many digits of precision were saved.
It's going to take time to do this, no matter what; if you can even manage to hold all the needed data in memory at once or not.
It probably is as fast to read the full file and then only keep the information you need from each in turn as it is to add the overhead of reading only part of the file during the input step.
Is there any real need to have all the data at one time--cannot it be analyzed/plotted/whatever piecewise?
A .mat file will certainly be quite a lot smaller and quicker to load than all the .csv files but of that size it still will be noticeable. The fastest possible would be fwrite, fread, a straight binary file. For a single array, this is trivial code.
