using System;

using System.Linq;

using System.Collections;

using System.Collections.Generic;

using System.Xml.Linq;

using System.Xml;

​

​

public class Program

{

    public static void Main()

    {

        var raw = @"<elem c='98500000'> 

  <elem c='98510000'> 

    <elem c='98511000'/>  

    <elem c='98512000'/>  

    <elem c='98513000'> 

      <elem c='98513100'/>  

      <elem c='98513200'/>  

      <elem c='98513300'/>  

      <elem c='98513310'/> 

    </elem>  

    <elem c='98514000'/> 

  </elem> 

</elem>";

        var doc = XDocument.Parse(raw);

        var list = new List<string>(){"98512000", "98513300", "98514000"};

        doc.Descendants()

            // all `c` value doesn't match current element's `c` attribute value

           .Where(o => list.All(c => (string)o.Attribute("c") != c) 

                            && 

            // and all descendant elements doesn't have matching `c` attribute value

                       o.Descendants().All(d => !list.Any(c => (string)d.Attribute("c") == c)))

           .Remove();

        Console.WriteLine(doc.ToString());

    }

}