How to either hide or delete specific computer files Time Machine

Hi i have a MBP late 2011 with 10.8.2 on it, and i use a time capsule to store a large amount of files that i use on both my mac and my windows 7 laptops. I am getting annoyed by all the unnessicary or junk files placed in all my stuff such as:
.ini
thumbs.db
.AppleDouble
.DS_Store
:2e*
I would like it so i just dont see these files on either my windows 7 computer or my mac. I have my folder options on my windows 7 laptop set to hide hidden files. Is there a way to set these files to be hidden on a PC? If not is there an application on either windows 7 or mac that can clean these files from my time capsule? I know how to use terminal and CMD well enough to do a step by step.... Also i know how to change windows registry on windows 7.
Summary:
Time Capsule used by both Windows 7 PC and MBP
Time Capsule is FULL of operating system files listed above
I want to hide or delete all of these files from existence on the time capsule for BOTH my Mac and my Windows 7 computers
If hiding them on windows/mac i would like to do this once and forever hold my peace
if deleting them it would be easier on me if there were either a Mac or Windows application or progaram that will do it
I can use CMD and Terminal very well, you wouldnt need to explain how to open them or such, just say a brief step by step.. Such as: 1) open terminal 2) "insert promt here" )3" next promt/ input"
On windows i have used Windows Registry many times to edit and tweak thingsdont have to explain anything- just post which Hikey to go to, what to search and then what to edit
Sorry that's a mouthful but i figured i can save the IT's/ DEV people out there some work by saying exactly what i want and what i know.

You cannot delete those files.. they are OS files, and created by the OS to track changes etc.
The Mac by default should not show hidden files. I am not sure why you are showing them unless you turned that on at some point.
http://apple.stackexchange.com/questions/58709/how-to-view-hidden-files-in-finde r
That includes the command to turn off show hidden files.
As for windows, the Unix type file marking will be completely unknown to explorer.. so you would have to go through each file type to hide extension. Windows by default nowadays does hide extensions.. if that is not working then I suspect it cannot actually recognise it.

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