How are the LEGO instruction manuals made? I wish to know how the LEGO instruction manuals are made. What is the process currently used?
How lego does it today.

I found little information about Autodesk Maya being the 3D modeling software being used. Here`s a blurb about their current design process : 


  Primary concept and development work takes place at the Billund
  headquarters, where the company employs approximately 120 designers.
  The company also has smaller design offices in the UK, Spain, Germany,
  and Japan, which are tasked with developing products aimed
  specifically at these markets. 
  
  The average development period for a new product is around twelve
  months, in three stages. 
  
  The first stage is to identify market trends and developments,
  including contact by the designers directly with the market; some are
  stationed in toy shops close to holiday periods, while others
  interview children. 
  
  The second stage is the design and development of the product based
  upon the results of the first stage. As of September 2008 the design
  teams use 3D modeling software to generate CAD drawings from initial
  design sketches. 
  
  The designs are then prototyped using an in-house stereolithography
  machine. These are presented to the entire project team for comment
  and for testing by parents and children during the "validation"
  process. Designs may then be altered in accordance with the results
  from the focus groups. 
  
  Virtual models of completed Lego products are built concurrently with
  the writing of the user instructions. Completed CAD models are also
  used in the wider organization, such as for marketing and packaging.


Source : wikipedia

How people do it themselves

LEGO provide software that does just that. Check for "LEGO Digital Designer" which allows to create a model, save a building manuals and buy the LEGO parts online.

Also check up this related question :"Do any programs exist that allow you to build own LEGO plans?"

For more information on how to create high quality computer images of LEGO models, check this question : "How can I create synthetic imagery (rendering) of lego models?"