I use Recognita 5.0 for that. The scanned document is transformed into text preserving its layout, and after that it can be saved in various file formats (including Excel file). Read more here: http://www.tabone.com.mt/software/recognita.htm
Unfortunately it's a discontinued product...
A demo version is still available for download here: http://dl.drenik.net/spawn/opis.php?id=1252 (but it won't help you much since in the demo version the save is disabled).
Recognita was bought out by Omnipage, so the new version of their OCR program offers the same functionality as Recognita had (but for much higher price ): http://www.scansoft.co.uk/omnipage/