1. You need vSphere CLI – Download Here
For Windows or Linux and install on your workstation.
2. Download the Upgrade Package for 4.0 to 4.1
3. Power off your VM’s and put the host into maintenance mode
4. From the vSphere CLI prompt
vihostupdate.pl –server hostname or IP -i –b d:\downloads\upgrade-from-ESXi4.0-to-4.1.0-0.0.260247-release.zip -B ESXi410-GA