To reset the content index of your Search Service Application, you can either use the UI as described in the following TechNet article, or use the following PowerShell command :

(Get-SPEnterpriseSearchServiceApplication).Reset($true,$true)

The Reset function takes 2 Boolean parameters :

- Disable Alerts

- Ignore Unreachable Server

 

This sample is for a Farm containing only one instance of the Search Service Application, if you have more than one you should adapt the sample.