I'm using CuteFTP ftp client since couple years ago. To make myself easy, normally I will directly drag the whole folder to remote server.
Eventually, I have found that I can use the filter function in the CuteFTP to avoid these files from being uploaded. It's pretty easy.
- Choose from the menu View > Filter to open the Filter page.
- On the Filter Properties tab, tick the follow options.
- Switch to Filter NOT Mask tab, and add in any file name you want to filter out during ur file transfer. I added "Thumbs.db", and it's not visible in CuteFTP client now.
- Now, you can doing batch upload with these unwanted files filtered.