Can I use Canon software to upload photos from a Nikon camera?

Can I use Canon software to upload photos from a Nikon camera? - 1

There's NO need to do that.

Just remove the memory card from your Nikon camera, insert it into a card reader, either the one on your computer or a USB 3.0 card reader you have purchased and then using your computer skills, copy all the image files from the card to a new file folder on your computer you have named for the subject'location and date so you can find those images years later.

You need to get out of the habit of using a "program" to copy images from a memory card. 1) the program will send the image files to a default folder and keep adding more and more images as you shoot more and more photos. 2) This makes finding specific photos problematic and 3) some software programs only look for still image or video image files, so one or the other is left on the card. Since you are supposed to format the card after safely copying all the image files from it, there's a good chance that you may lose files not 'seen' by a specific program

The problem with attempting to use Canon software is that it only recognizes Canon subdirectories on a memory card and only Canon RAW (CR2) files, not Nikon RAW (NEG) files.

No. As fhotoace wrote, you do not need any specialized software to download files from an SD card to a computer. All you need is an USB card reader. Just plug it in and your computer will automatically load the drivers for it. Plus, depending upon your computer, if you get a USB 3.0 card reader, it will download data 10x faster than the USB 2.0 technology found in digital cameras.

Even with a Canon camera, you shouldn't be doing this. Use Windows Explorer or (Mac) Finder instead for more control over what goes where exactly and to absolutely certain picture quality does not change.