Align With Writing on the Ball
If you look at most golf balls, you'll see writing on the ball. This writing is normally printed in a straight line, so you can use it to aim at your target. Align your putter face perpendicular to the writing. If you have a line on the top of your putter, you can use that line to align directly with the writing on the ball.
Spot putting is another easy way to improve alignment. Look down your target line and pick a target. Try to pick a spot a few inches in front of the ball. It's much easier to aim at a target that is a few inches in front of you than a target much farther away.
Check Your Eyes
When your eyes are directly over the ball, it's easier to see the proper line. Many players set up with their eyes inside or outside the ball. To check your eye alignment, take a ball and hold it under your left eye. Drop it and see where it lands. If it falls straight down on the ball, your eyes are properly over the ball.