InDesign CS6 PDF Issue: Unsearchable PDF document

Question

Hello all,
I have an issue that I've exhausted with days of Google searches. I have a text catalog created with ID CS6. Sections were PDF documents given to me from our engineering department. The book was created, exported and all went well until I found out that when I try to copy and paste the text into Microsoft Word or Note Pad, I get a lot of small boxes in place of the letters. When I try to search the text in Adobe Reader, I can't find words which I can see are there.
This is the first catalog I've created in CS6. Previous catalogs created in the exact same manner in CS4 & CS2 do not have this issue. I thought it could have been the infamous Arial Narrow font issue and researched that to death.
Any ideas would be most helpful. This is a 1300 page catalog that customers cannot search.

Answer 1

1. LAUNCH Adobe Acrobat
2. Using the File menu, OPEN the corrupted document. (I don't know what to do if you're not even able to open the file. Sorry!)
3. (VERIFY that Acrobat can't search the document, in case you haven't done so, just to avoid unnecessary work.)
4. EXPORT: Once the document is open, use the File menu again, and choose EXPORT / IMAGE / PNG. Your corrupted pdf will be saved as a series of images with the file extension ".png", one for each page of the pdf document. Don't worry, they will be numbered automatically by Acrobat, and they aren't terribly large. My document was 200 pages long, so I got 200 little image files in .png format. The export may take a couple of minutes. You won't get any further signals from Adobe to tell you it's done--just go look in the directory that contains the original and see if it made png files with names like:
chemistryBook_Page_001.png
chemistryBook_Page_002.png
5. COLLECT: Once you have the image files, collect them all by cut and paste into their own directory.
6. OCR: Under the Document menu, choose OCR TEXT RECOGNITION / RECOGNIZE TEXT IN MULTIPLE FILES USING OCR
7. ADD FILES: You will be shown a dialog box with the title "Paper Capture Multiple Files" with the subtitle "Run OCR on a set of images. There is a button that says "Add Files". Click this button, choose ADD FOLDERS, and browse to the folder that contains your png files. Highlight that file, click OK. The files will then appear within this dialog box. Make sure that the files are in the proper order, or you will be sad. Click OK.
8. CHOOSE OUTPUT OPTIONS: Now you will get a dialog box entitled "Output Options". You have several choices to make here:
TARGET FOLDER: Click "Specific Folder", then Browse to your folder full of images, click "Make New Folder", name the folder (something like "CHEMISTRYBOOKIMAGEFILES" so you can find it easily and know what is in it, click OK.
FILE NAMING: Click "Keep Original File Names". This will preserve Acrobat's automatic numbering of your files--you will need that to get the page ordering right! UNcheck "Overwrite existing files" just to avoid a terrible mishap, unless you are very pressed for disc space or unless this is your 5th time attempting to follow these instructions and you've already got 'way too many duplicates of the output files. If you have the disc space, just make new empty folder for your 6th try.
OUTPUT FORMAT: Select "Save File(s) as Adobe PDF. Click OK.
Now wait for Adobe to execute optical character recognition on the image files. Its output will be one little pdf file for each little image file that it OCR's.
9. COLLATE THE FILES INTO ONE: Under the File menu, select COMBINE / MERGE FILES INTO A SINGLE PDF. This step is optional; maybe you wanted a bunch of little files, or maybe you wanted to divide your enormous original document into 2 or 3 more manageable documents. To divide the file, just make a separate directory for the png files you want in each smaller final document, and repeat steps 6 through 9 for each directory. BE CAREFUL WITH NAMING! Make sure you choose a unique name, because if you got something wrong, you will want to be able to go back to your original corrupted pdf and try again. If your original is named "CHEMISTRY.PDF", please remember to name this new file something like "CHEMISTRY-FIXED.PDF".
If you really despise pdf, you can try using different output formats in Step 8. I do hate pdf, but I chose pdf for two reasons: one is that I had more confidence that that pdf would retain important features like charts and graphs and labeled photos in my document. The other is that I was so so so so SO tired of doing all this pdf crap instead of the chemistry work that I'd gotten the ebook to help me with that I didn't want to do anything fancy with file formats at this point. Let me know if you try output to rtf or ascii and get good results.
10. TEST: Open the merged document(s) in all of the pdf readers and web browsers you will want to use with it, and try searching with it. Use your file browser and try to search for text in the directory with a word you know the file contains. Searchable? Good job, you're done, cheers!
Not searchable? Oh noes! Check that you opened the correct document (maybe you opened the original by mistake). Try the entire process again. If that doesn't help, try the entire process again, but output to plain text this time. My apologies, but, being a complete newbie myself, I have no further advice on this topic.
NB! My output PDF is of rather low quality. It looks like it was literally scanned from a 10th-iteration paper copy. Don't know how to fix that, after the fact or somewhere in the above process. It's good enough, so I'm just dealing with the shakey blurriness. I seem to remember somewhere that I could choose a high quality output, but, again, I didn't want to do anything fancy with vectors and rostering and layers and other terms that I don't know before I verified that I could do something basic and get back to chemistry asap.