The gist below will copy all html files from one directory to another keeping the directory structure in place

Copy-DirectoryStructure

function Create-WebSite
{
    Push-Location ..\

    $webSiteContainer = "WebSite"
    Remove-Item .\$webSiteContainer -Recurse -Force

    New-Item -ItemType "directory" -Name $webSiteContainer | Out-Null
    $items = Get-ChildItem -Recurse -Filter "*.html"   

    foreach ($item in $items)
    {
        $itemRelativePath = $item | Resolve-Path -Relative 
        $itemRelativePath = $itemRelativePath.Remove(0,2)
        $containingFolder = Join-Path $webSiteContainer $itemRelativePath.Replace($item.Name , "")

        if(!(Test-Path $containingFolder))
        {
            New-Item -ItemType "directory" -Name $containingFolder | Out-Null
        }

        Move-Item -Path $item.FullName -Destination $containingFolder -Force
    }    

    Pop-Location
}