I've not been able to duplicate the problem and so I can't offer any direct advice on it.
You can get dedicated uninstallers which claim to be able to remove all trace of a program from your PC, but most work best if they are installed prior to the program you ewant to get rid of, since they often worki by cataloging which files go where and when they went there.
If you have Windows XP you could always try a System Restore, but you might lose other programs, settings and files by doing so.
I tried WISE-FTP a year or so ago out of curiosity when I got if free with a 1&1 domain and it has a very quirky way of doing what it does. After playing with it for a few days I decided that it was not for me. It did uninstall cleanly though.
My all time favourite FTP client is WS_FTP Pro from Ipswitch. I can't praise it highly enough and it has served me well for years.
One of the support questions on the WISE-FTP site suggests downloading the very latest version, running the installer and attempting to uninstall the prior version with the latest one which they say has this feature. They also suggest:
If you wish to uninstall the application, open the Windows Explorer and delete the file wise_click here in the folder c:\program files\acebit\wise-ftp. Now you can restart the installation program to deinstall WISE-FTP.
This is meant for a slightly different problem to yours, but try renaming the wise_click here file to wise_click here or wise_click here then download the latest version, run the installer and see if there is an option to uninstall the previous version.