re Little black boxes

Hi Everyone
Greetings from Ireland!
I was wondering if anyone could clear this up for me.
I had a site up on the web. It was created by hand using html and notepad as
the editor.
I wanted to make a few changes to the site and downloaded it this morning.
Now, however when I want to view the source code to tweak it a little - I
see all these little black boxes. They seem to be marking the blank spaces
in the text. Is there any  quick way of removing them so I can work with the
text? Or can it be avoided in the first place ?. Interestingly it has not
occured on all the pages of the site.
Thank you in advance. I have learnt so much from this group.
Ber Fen

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