There's not a way to clear points out entirely because the points are attached to specific things (i.e. events, behaviors, etc), but you can set up Recognition Periods for each quarter/semester.
After you've set up the different periods, you can set up rewards and run reports and/or leaderboards by Recognition Period.
If your school assigns point values for Activities, the points will carry over through each Period because there is not a date attached to them. For example, if a student earns 50 points for being a member of a club, those 50 points will appear in each Recognition Period.
To learn more, view our help documentation: Recognition Periods