You haven't shown any code, and your description is pretty woolly, but as of .NET 4 this would be a very easy way to do what you want:
IEnumerable lines = File.ReadLines().Where(line => line != "");
Note that it won't perform any trimming, so a line with only spaces in would still be returned.
Also note that the code above doesn't read the file when you just execute that line - it will only read it when you try to iterate over lines, and will read it again every time you iterate over lines. If you want to read it into memory all in one go, you might want:
List lines = File.ReadLines().Where(line => line != "").ToList();
