Stop your server before you start to clean.
Stopping a server
You can stop the server from the Servers view.
To stop the server:
- In the Servers view ( Window > Show View > Other > Server >
Servers > OK), select the server that you want to stop. - Click the Stop the server
icon
in the toolbar. In the Servers view, the status of the server
changes to Stopped. -
If for some reason the server fails to stop, you can terminate the
process as follows:a. Switch to the Debug perspective.
b. In the Process view, select the server process that you want to stop.
c. Click the Terminate

icon in the toolbar.
Note: When terminating a server, the server process will end and the server will not go through the normal routine of stopping, for example calling the destroy() method on a servlet.
Source: Eclipse Help