Kindly provide suggestions on how to permanently remove these files or on how to remove the modified files in windows registry.
You do NOT need to remove files or registry entries manually.
From Microsoft's site: Warning**Serious problems might occur if you modify the registry incorrectly by using Registry Editor or by using another method. These problems might require that you reinstall the operating system.
You've only killed the running processes so far. Until you remove the malware that's creating those processes and registry entries, it'll likely keep appearing in startup. What you need to do is run anti-malware scans to remove the malware permanently that's creating those processes.
First, open Control Panel. Under Programs and Features - Uninstall a program, check for anything suspect and remove/uninstall it. If unsure, leave it alone. Note: This will only 'start' the uninstall process. Then run Disk Cleanup to clear out temp, temp internet files, cookies, etc.
After which, run Rkill again if necessary to kill those processes before running these malware removal programs.
How to Remove Adware from a PC
How to find and clean malware infections with Emsisoft Emergency Kit
Edit: Just FYI, I Googled a couple of those entries. According to Symantec, one of those entries: Trojan.Egguard is a Trojan horse that downloads malicious files and injects malicious javascript into web pages on a compromised computer. Trojan.Egguard Another site says it's PUP.
It may be necessary for you to seek further help on a specialty forum if those steps don't get rid of it. Let us know how things go after following above steps.