Deleting an old application?

I recently used a harddrive to back up my computer, which used to be for a really old Mac I have in my basement. I wanted to zip the files that were backed up from the old computer (OS 9), so I brought them onto my Mac to compress them. Once done I moved the .zip back onto the drive and dragged the uncompressed compressed folder into my trash. I tried deleting it, but it told me "VistaScan Installer couldn't be deleted". At first I thought it was open for some reason, so I got a live list of all processes, - nothing. I tried restarting my computer, then deleting, - still nothing. I could force-delete the file with Terminal, (sudo rm /path/to/file.app) but I'm really uneasy using Terminal again. Last time I did I destroyed my Mac, lost every file and had to start over. (It's why I wanted to back up, to prevent it from happening again.) How do I delete the file?