Since esxi4.1 does nto have a console you will need to run mbralign from some sort of linux machine. vma will work. make sure you mount the datastores accordingly.
Example perhaps you can do soemthing like this:
create a NFS datastore and call it 'alignNFS' for example. storagemotion your machine into that datastore to perform the align (its not necessary but gives you an area to perform this so you can keep things organized. after the alignment process is done (the machine will need to be off when you perform it. ppower it on test the storage motion machine back. then go to your 'alignNFS' datastore and delete the backup files the alignment process created.
to check if the machine requires an alignment you simply type: (from the linux or vma machine)
you will get a result of either aligned 'Yes' or "No"
to align the machine
mbralign --sparse machinename-flat.vmdk
if it has more than one virtual disk then you will see something like
mbralign --sparse machinename-flat_1.vmdk
the scan can be performed while it is on but the alignment process the machine needs to be off
this has been asked many times but I will put it here in all caps as I am not yelling or trying to be rude but just as a note..
*** MS OPERATING SYSTEMS OLDER THAN WIN2K8 and WIN7 NEED TO BE ALIGNED ***
If your create a win2k3 template with one drive and have it aligned then later add another drive to it when its a virtual machine then that drive will also need to be aligned.