Some temp files are created as soon as you start the computer. They cannot normally be deleted until the next session.
Yes trojan installer files can hide in these folders but any good anti-virus and anti-malware scanners can find these and neutralise them.
Many use a dedicated temp file remover, and for Windows users we often recommend CCleaner from http://www.piriform.com/ccleaner . It will delete all temp files, all Temporary Internet Folder files, all unwanted cookies, (you can tag favorite cookies to prevent them from being deleted), and other cleanup options.
I run a PC Laptop, HP6510B. My question is why some temp files, cookies and prefetch folder files will not delete, even well I dont have any programs open.
Do you think these can be trojans or other viruses hiding in these folders and immune to deletion? or are they more likely related to programs that are kind of running in the background?