This is an example script that clones a VM, but excludes the 2nd harddisk.
You can of course change the selection criteria for the to be excluded harddisk(s).
$srcVM = 'VM1'$tgtVM = 'VM2'
$tgtFolderName = 'TestFolder'
$tgtDatastoreName = 'TestDatastore'
$excludeHD = 'Hard disk 2'
$vm = Get-VM -Name $srcVM
$tgtFolder = Get-Folder -Name $tgtFolderName
$tgtDS = Get-Datastore -Name $tgtDatastoreName
$spec = New-Object VMware.Vim.VirtualMachineCloneSpec
$config = New-Object VMware.Vim.VirtualMachineConfigSpec
$hd = Get-HardDisk -VM $vm -Name $excludeHD
$devChange = New-Object VMware.Vim.VirtualDeviceConfigSpec
$devChange.Device = $hd.ExtensionData
$devChange.Operation = [VMware.Vim.VirtualDeviceConfigSpecOperation]::remove
$config.DeviceChange += $devChange
$spec.Config = $config
$location = New-Object VMware.Vim.VirtualMachineRelocateSpec
$location.Datastore = $tgtDS.ExtensionData.MoRef
$spec.Location = $location
$spec.PowerOn = $false
$spec.Template = $false
$vm.ExtensionData.CloneVM($tgtFolder.ExtensionData.MoRef,$tgtVM ,$spec)