As mentioned earlier it is possible to work with different virtual models depending on each other applying different/more refactorings and/or resolutions.
There are 2 built-in virtual models:
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Parser is the model that is generated by the language specific parsers without structural changes or any resolutions for created issues.
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Modifiable.vm is the (initially empty) model ready to save any refactorings or created resolutions by the user. It naturally depends on the Parser model.
The user is free to create additional virtual models.
NOTE A virtual model might affect metric values since the structure of the system can be changed with refactorings and issues can be transformed into tasks or ignored. So, depending on what you want you should select the corresponding virtual model. If you want to see the unaltered metrics and structure you should select the 'Parser' virtual model (or an 'empty' virtual model - without any refactorings or resolutions). In the user interface you can either select the virtual model in the right-hand side drop down menu in the upper toolbar or in the Files view on the left hand side underneath the Models folder with the corresponding context menu entry.