Windows stores the information in the Registry, which means that there are manual and automatic ways of manipulating the data. You could run a program like CCleaner, AppCleaner or SlimCleaner to remove the entries automatically, or open the Windows Registry Editor to edit single entries or all manually. That is, if you know where Windows saves the Run MRU information. MRU stands for Most Recently Used.

The Windows Registry location of the Run MRU is:

HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\RunMRU

Windows Run History Editor is a free portable editor that allows you to edit, add or remove Run MRU entries. All existing commands are displayed automatically on program start.

Each command is listed in its own editable field. To edit an existing command, click into the field and use the keyboard to change it. You can also remove commands by clearing their fields, or clear all data automatically with a click on the clear all data button.

A click on Save writes the changes to the Windows Registry, so that they become available immediately on the system. There is also a reload button to load the active settings again in case you made an editing mistake and want to load the current settings again without saving the edits.

The program basically acts as a frontend for the Registry Editor which is not that comfortable to edit.

Windows Run History Editor is a free program that is compatible with 32-bit and 64-bit editions of the Windows operating system. It requires the Microsoft .NET Framework to be installed on the system. The developer does not mention which version on the project homepage. The program can be downloaded from Sourceforge.

Indo Cleaner is a privacy software that can deal with most recently used file listings. It basically is a cleaner that checks various lists for entries giving the user the option to delete some or all of them so that they cannot reveal any information about which files have been opened in the past.

All available mru lists are selected by default after installation and start of Indo Cleaner. This includes Windows Explorer, Internet Explorer, Microsoft Office and Windows Media Player but also Firefox and Opera. It is possible to uncheck any of the programs listed to prevent the lists from being cleaned up.

The remaining most recently used lists will then be checked and the number of entries that are stored in the Windows operating system are shown. Here it is again possible to uncheck some programs or proceed with the cleanup to delete the selected recently used files.

Indo Cleaner is not the only privacy software that can clean the most recently used files. Ccleaner is for example another program that can delete those files. Indo Cleaner (via Into Windows) is compatible with Windows XP and Windows Vista (and likely Windows 7).