You question isn't very clear, but if you're talking about searching in an encoded string, I don't think you have a choice but to decode it and then search. It isn't that complicated though:
public static void SearchInBase64(string encodedData, string searchText)
{
byte[] encodedDataAsBytes
= System.Convert.FromBase64String(encodedData);
string decodedValue =
System.Text.ASCIIEncoding.ASCII.GetString(encodedDataAsBytes);
// Perform search on decodedValue
...
}
Update: Based on your updated question, if you want it to run directly from the VS2010 IDE. Create a simple program based on the above logic which receives the 2 strings from the command line. Then add that program as an external tool using:
Tools -> External Tools