I found this post that also works for Share point 2013.
according to that, we can do this :
- Launch the SharePoint 2010 Management Shell with administrator privileges (Start -> All Programs -> Microsoft SharePoint 2010 Products -> Right click on SharePoint 2010 Management Shell -> Run as administrator).
- Run 'Get-SPServiceApplicationPool'.
- Run 'Get-SPServiceApplicationPool -Identity <"Name of the application pool">
- Run ‘Remove-SPServiceApplicationPool’.
- Input the Identity <"Name of the application pool">.
- Input 'Y' to delete the application pool.