You can bookmark regions on the timeline by clicking and dragging, then clicking the pencil icon in the top left corner. You can then enter a name for your region so you can select it again later.
When you select a region profiling results will be displayed for that region, so it's best to do this whilst your application is relatively idle in order to avoid skewing the results. You could get around this by selecting a very short period of time, and using the region just to bookmark one end of a time period of interest.
Hope that helps.