There's an example in MSDN (click here)
I think the example is self-explanatory, but here's the excerpt:
using System;
using System.Security.Cryptography;
using System.Security.Cryptography.X509Certificates;
using System.IO;
public class X509store2
{
 public static void Main (string[] args)
 {
  //Create new X509 store called teststore from the local certificate store.
  X509Store store = new X509Store ("teststore", StoreLocation.CurrentUser);
  store.Open (OpenFlags.ReadWrite);
  ...
  store.Remove (certificate1);
  store.RemoveRange (collection);
  ...
  //Close the store.
  store.Close ();
 }    
}