If you want to create a tile, you can do it like in this answer :
SecondaryTile tileData = new SecondaryTile()
{
TileId = "MyTileID",
DisplayName = "MyTilesTitle",
Arguments = "Some arguments"
};
tileData.VisualElements.Square150x150Logo = new Uri("uri to image");
await tileData.RequestCreateAsync();
If you want to delete a fragment, you will need to find your tile (for example, by its identifier), and then call RequestDeleteAsync():
SecondaryTile tile = (await SecondaryTile.FindAllAsync()).FirstOrDefault((t) => t.TileId == "your tile ID");
if (tile != null) await tile.RequestDeleteAsync();
MSDN.