From application list deployment can be deleted.
If application need to do actions before delete it, uninstall.cmd file can be to use to include require actions.
For example, if application is a windows service, before delete it service must be stopped and deleted.
uninstall.cmd
NET STOP "AzureMultiApp.Service"
"%Windir%\Microsoft.NET\Framework\v4.0.30319\installutil" /u "WindowsServiceSample.exe"
ERRORLEVEL == 2 EXIT 0
IF ERRORLEVEL == 9009 EXIT 0
IF ERRORLEVEL == -1 EXIT 0
:end