I need to know how to clean noise from an image with Matlab.
lets look at this example:
Did you start with a bilevel (two color, black and white)? Or did you threshold it yourself?
If it's the latter, you may find it easier to perform noise reduction before you threshold. In this case, please upload the image you have before thresholding.
If it's the former, then you'll have a tough time as traditional noise reduction is concerned. The reason is that a lot of noise reduction approaches take advantage of the distinction in statistical properties between the noise and the actual natural image. By thresholding, that distinction is essentially destroyed.
EDIT
OK, technically, your image isn't really noisy -- it's blurry (letters are running into each other) and has background interference.
But anyway, here is how I would deal with it:
Green channel:

Blur (5x5 Gaussian):

Thresholded image (I used a threshold of ~93 in GIMP):

Final result:

You can see that the gaps in the middle 6 and 9 have dissapeared. Unfortunately, I couldn't get the gap in the left 3 to go away -- it's simply too large. Here's what the problems causing this are: