PDFs are a great archive format for scanned images, but Acrobat does not allow you to edit the text layer of the document (the part that can copy and paste from) leaving you with just the raw OCR. Are there any freeware alternatives that let you edit the text layer?
Free PDF editors are very scarce.
From the techsupportalert article A PDF File Allows Editing in 100% Layout Accuracy:
A scanned document converted into a PDF initially does not contain any text. It's composed of pages each covered by a full-page pixel image. This image may or may not contain areas that look the same as shapes of characters, identified by human brains as letters and "text".
Programmatically, it is not text, only pixels.
In order to insert into a PDF derived from scanned images something that is real text, one can only employ an OCR process. This will add an extra layer of content to the PDF pages. That extra layer would contain all identified (or mis-identified) characters behind the pixel shapes as real glyphs from a real font. However, these real-text characters do have a special PDF markup, tagging them to not be rendered visually by a viewer (or when printing). Their existens would show up only when searching (or highlighting) text (or when trying to copy'n'paste areas from the image while the Acrobat Text Touchup Tool is active).
So, is your real question this: "The OCR results for my scanned PDF documents are sub-optimal. Not all characters are correctly identified. I want to edit the hidden text in order to make OCR result better. How do I do that with a free tool?" ?
Edit: I'm not normally using Acrobat. But just now I had the opportunity to look at a 9.1.3 Professional version on a collegue's PC.
First thing I checked: Is it really true, that Acroabat doesn't allow to edit OCR'd text?
Answer: No, not true. I could use Acrobat's builtin OCR engine to capture the text of a random scanned document which I google-searched and downloaded from the web. After that, this text was perfectly editable with the TouchUp Text Tool available via the Advanced Editing menu entry.
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It appears what you mean by "text stream" is the text data from the PDF. Not sure. If that is the case, I use the standard clipboard and any text only editor, I use KEDIT because of it's column editing capabilities, to capture the data and edit it. The problem is that you lose any formatting with this and sometimes with tables the order of the data get messed up. But, for simple captures, it works.