During the monitoring process MSI Package Builder records the modifications performed by all processes that operate in the system. Thus monitoring results can include the modifications performed by system processes. These modifications do not refer to the application or installation that you have monitored and that is why they should be excluded from monitoring results. This goal can be reached using the Monitoring Processes Filters configuration. While using process filters, the changes made by those processes are automatically excluded from the resulting deployment package. In the same manner, there are registry keys and file system paths that should be excluded from the resulting deployment package. The Monitoring Registry Filters and Monitoring File Filters configuration allow you to fulfill this.
When the installation creates a joint resource that is commonly used by several applications, such resource should be indicated as permanent. Permanent files, keys and registry entries are not deleted during application uninstall process to prevent functionality violation of applications that use these resources. You are able to set permanency option for each resource in separate during its edit but it seems to be quite a complex way. To simplify the operation with permanent resources MSI Package Builder comes with a set of predefined uninstall filters and allows you to add some.
All the filters in MSI Package Builder are set up in the program preferences. Press the Preferences button from the Application Menu and you'll find the filtration settings under the Filters group.