You can simple split the XML string by blank and remove the part with "xmlns:xsd":
string strXml = "<Root xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xmlns:xsd='http://www.w3.org/2001/XMLSchema' Version='V1.0'></Root>";
string[] ar = strXml.Split(' ');
string strResult = string.Empty;
foreach (string str in ar)
{
if (!str.Contains("xmlns:xsd"))
strResult += str + " ";
}