Hi Luis,
For a single wave file use the following commands at the command line:
mkdir new
[this creates a new folder named 'new']
autoloop 036-c.wav /o new/036-c.wav
[this executes autoloop.exe and tells it to look for loops in a wave file named 036-C.wav and outputs the looped file to the new folder]
Hope that helps,
GrahamG