Those files are used to hold customization options when you use the Web View for folders. If you want to get rid of them, you'll have to use the Windows Classic view.
-= Customizing Web View =-
Folders can be individually customized by opening the folder and selecting the Customize This Folder option in the View menu. When this option is selected, the Web View Wizard is launched. After the wizard is completed, two new files are created in the target folder: Desktop.ini and Folder.htt.
* Desktop.ini *
The Desktop.ini file is a standard .ini file, used to tell Internet Explorer that a folder has a customized Web View. Each customized folder has one Desktop.ini file. The shell reads the Desktop.ini, which directs the shell to host the MSHTML.dll component of Internet Explorer 4 and points it to the appropriate .htt file.
This is a sample Desktop.ini file:
* Folder.htt *
The Folder.htt file is a template that contains customized HTML content and an ActiveX control to display the normal directory listing. Each customized folder has one Folder.htt file. It is the same file referenced in the PersistMoniker=file://folder.htt desktop.ini setting earlier on this page. To create Folder.htt, the Web View Wizard launches your HTML editor with the <windir>\Web\Folder.htt template. If you save the default HTML provided by the wizard, the folder will appear the same as it did before you ran the wizard. The Folder.htt template file can be edited at any time, and it is liberally commented so you can find your way around in the file. A sample of an uncustomized Folder.htt file can be found in the <windir>\Web\directory.