I had a script that used to upload screenshots in a Screenshots directory and it was supposed to contain the screenshots only (no other subdirectories). Something happened to that script that it started uploading one directory for each screenshot, so if there were 500 screenshots, there were 500 directories and each one contained a single file.
I solved this by mounting my Drive like @calisro suggested and then used this command to download them all locally without the unnecessary dirs:
find . -type f -exec cp {} /Users/andyibanez/Desktop/gImages \;