From Console you can try the following
Login to Console
Under Enterprise->Monitoring->Click on Incident Manager menu item to go to the Incident Manager UI and then click on "All open problems" link on the left
Identify the specific problems for your target.
Click on the problem link to show details
On the Right Hand Side, you should be able to Clear the problem which will clear all Incidents associated with the problem.
Navigate to the Target Homepage
Click at the target level menu and navigate to Monitoring -> Incident Manager => Click All open problems on the left and identify the problem from there -- Click on the problem link to show details --> You should again see the clear option enabled to clear the incident here
Also you can refer to below metalink doc to understand which metrics in Cloud Control can be manually cleared if required
What are Statefull and Stateless Metrics in Enterprise Manager - Explanation and Example (Doc ID 733784.1)