Before you attempt deleting empty folders and zero-byte files, check with Windows Prime gurus to make sure you do not accidentally step on Superman-- Windows' cape. If you do, you might find yourself starting a thread on fixing broken Windows operations. Give us a few names of the folders and files you have found -- some I may recognize even though I'm a Windows 7 person.
well-balanced, well-configured mult-layered defense is best
From MS-DOS 3.3, MS-DOS 6.22, from Windows 3.1 to WFW 3.11 to Windows 95-98SE, now to Windows 7 Pro.
Security for now: Windows 7 Firewall, Emsisoft AM, MSE [scan-only], SpywareBlaster, Ruiware/BillP combine
CCleaner is relatively safe. Manual deletion of empty folders or zero byte files is risky. If they belong to the system this is asking for trouble. Empty application created folders may appear to be unused but may later be needed and the results are unpredictable if they are not present. Zero byte files may serve an important purpose.
Considerably more information is needed before anyone could help with manual deletion of such items.