Hi Wai Wai
If you are referring to rootkits, then when your'e dealing with kernel-mode rootkits there may be nothing that can fully detect them or their hidden process and files, while running detection tools inside the operating system you suspect has those hidden files/folders..
A little info on rootkits:
http://www.bluetack.co.uk/forums/index.php?showtopic=8604Here's a few tools that may be what you are looking for:
http://www.spywarewarrior.com/viewtopic.php?p=116213#116213Most of the tools I like to use are all listed in this guide, and suit various situations for digging things up that may be hidden otherwise:
http://www.bluetack.co.uk/forums/index.php?showtopic=4138The sysinternals tools are very handy. GMER, Icesword , Darkspy etc also have their uses.
Running a search through directories in dos can sometimes find things that dont show up normally and the various rootkit tools are another way of digging stuff out.
Rootkit authors are always finding new ways to bypass those so you can't rely on them 100% and there are an ever increasing variety of rootkits being designed and modified..
I always try to keep a record of the system files and directories for comparison along the way , things like bb filemap and sentinel 2.0 can log new files that are introduced into the system on reboot / shutdown.
Using something llike BartPE to search the system from outside the system itself if would be another way to detect hidden process/files:
http://www.nu2.nu/pebuilder/http://www.ubcd4win.com/