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To convert from column-major order (frequently found in reference files downloaded from on the internet) to row-major, the first step is to open the downloaded file in Excel. Reference files often include extra data. Here is an example from the Image Engineering TE262 Universal Test Target file, used for evaluating scanners. The color pattern in the large UTT chart is shown belowon the right. (There are two of these in some printed charts.)
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Here is a portion of the reference file, opened in Excel. We want to extract cells B7 through D33 (27 rows, 3 columns in column-major order). In this case, we are using the generic (typical; not individually measured) data, shown with the blue background.
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Because of the simple repetition in column 4 (mostly increments of 3 columns), it’s a lot easier than copying and pasting lines. Now Select the full 27 lines and 4 columns, right-click, and press Sort > Custom sort. This opens the Sort window. Choose Sort by Column D, then press OK. This sorts the data so that column D is in sequence, 1, 2, …, 27.
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Now select columns 1-3 (A1:C27), copy them, paste into a blank worksheet, and save as a csv or txt file. You have a column-major reference field. 
. Here is an example from Color/Tone Interactive.
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See Also
Colorcheck Reference File (legacy module: Color/Tone is recommended for new work)
Measuring Test Chart Patches with a Spectrophotometer for details about how to create a reference file using measurements from an instrument.