It is a good attempt that you made here with FOPEN and FSCANF; we can discuss the format if you want, but I would recommend using TEXTREAD in this case, which would simplify the process:
[dateString, timeString, flow] = textread('myFile.txt', '%s %s %f', ...
'delimiter', ',', 'headerlines', 2)
So here you have a one shot operation that opens/reads/formats the whole file, whereas you would have to read the file line by line and build arrays by yourself if you were using FSCANF.