You may not want your custom branding to apply to the application pages, normally the way I do this is by not applying custom master page to SharePoint 2010 as the System Master Page. But wait, although this method prevents the application pages from showing the custom branding, but it also prevents the branding from showing on any nonpublising page too :(
I found a better way to do this that is by stop master pages from applying to application pages by turning off the feature completely from Central Administration, as follows:
- Open Central Administration on the SharePoint server.
- Under Application Management, click Manage web applications.
- Select the desired web application from the list, and then from the ribbon, click General Settings.
- In the dialog that appears, scroll down to Master Page Setting for Application _Layouts Pages and select No.
- Scroll to the bottom of the dialog and click OK.
Now custom master pages for this entire web application will not apply to the application pages.