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 ();
}
}