When you have hundreds of image files organizing them requires some thought on your part. It’s a good idea to create folders and subfolders for each group of files. This way you can locate them more easily and you are less likely to fill up your HDD with a clutter of files that you have lost or forgotten about. Still, there are situations when probably there is no way to create a subfolder for some group of files, because they have nothing in common. ImageConverter Plus is able to convert the files from the folder ignoring subfolders. The more detailed instruction on how you can do it can be found here: http://imageconverterplus.com/help-center/work-with-icp/examples/recomendation/block-in-subfolders/