SpeedUpMyPC 3.x is a powerful and highly customizable application when it comes to cleaning unwanted files from your machine. In order to fine-tune the default settings according to your needs, open SpeedUpMyPC and click on the "Clean Up" tab. On the left side you will see a menu with "File Clean Up" as the first entry.
Click on "File Clean Up" to get to the list of junk files SpeedUpMyPC will look for. Notice that these 5 different categories can be individually selected or unselected, so if let's say you do not want the scan to detect "Lost Clusters" you can untick this option from this panel so as SpeedUpMyPC ignores any such files found. Further to this you can even customize which type of files fall under each category. If you click on the word "Lost Clusters", you will see that by default, lost clusters include any files with the extension "*.chk". You can add/edit this list by including or removing entries. If you click the "Default" button, all your changes will be undone and the default settings loaded. Another important and powerful feature is that you can omit any directories from being included for any particular category. To do this click on the "Ignore" button on the lower right corner and you can add a list of folders to be omitted from that particular category.
The "Privacy Protector" section is also somewhat configurable in the sense that you can select which areas you want to clean, such as "internet history", "cookies" etc.. To access the Privacy Protector, click on the "Clean Up" tab and then on "Privacy Protector" on the left. Each of the 12 different categories can be switched on or off. When a category is on (ticked), files and settings falling under that category will be removed from your system.
Also note that by default any junk files deleted are placed in the recycle-bin. These can be restored back as long as the recycle bin is not emptied.