You may easily use data downloaded with Historical Quotes Downloader with MetaStock software. You will have to convert data from ASCII format into MetaStock format using a free software from Equis International, MetaStock Downloader available at http://www.equis.com/
You will have to download and install MetaStock Downloader if you need stock quotes in MetaStock format; MetaStock Downloader will do data conversion. 

First of all make sure that you are using Historical Quotes Downloader version 1.21 or later. Start Historical Quotes Downloader and follow the steps below:
1) On "Download Settings" tab check "MetaStock" checkbox.
2) Open a symbol list file or add symbols and download historical stock quotes for them
3) Now run Metastock Downloader and select "Tools" - > "Convert" . A conversion dialog shown below will appear.

Select data folder for Historical Quotes Downloader and specify the extension, e.g. *.txt
Specify output folder for the converted files to be saved at, e.g. "C:\MetaStock Data". Click Browse button and add just downloaded historical quotes files. You may use "Shift" and arrow keys on your keyboard to select multiple files at once.

4) Now select "Options.." button A dialog shown below will appear. Choose Date Range, put a checkmark against "Traverse folders" and specify periodicity.
  

 
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