Thanks for your help. Unfortunately this does not work.
As you had suggested I created a bootstrapper file. Located it in c:\
Changed to the V3.5 of the framework directory and ran msbuild with the
argument bootstrapper file.
Here is the output.

-----------
C:\>cd C:\Windows\Microsoft.NET\Framework64\v3.5

C:\Windows\Microsoft.NET\Framework64\v3.5>msbuild.exe c:\mybootstrapper.xml
Microsoft (R) Build Engine Version 3.5.30729.4926
[Microsoft .NET Framework, Version 2.0.50727.4952]
Copyright (C) Microsoft Corporation 2007. All rights reserved.

Build started 9/16/2010 3:43:36 PM.
Project "c:\mybootstrapper.xml" on node 0 (default targets).
c:\mybootstrapper.xml : warning MSB3155: Item 'Microsoft.Net.Framework.3.5'
could not be located in 'c:\'.
c:\mybootstrapper.xml : warning MSB3155: Item
'Microsoft.Windows.Installer.3.1' could not be located in 'c:\'.
c:\mybootstrapper.xml(34,5): error MSB3147: Could not find required file
'setup.bin' in 'c:\Engine'.
Done Building Project "c:\mybootstrapper.xml" (default targets) -- FAILED.


Build FAILED.

"c:\mybootstrapper.xml" (default target) (1) ->
(Bootstrapper target) -> 
c:\mybootstrapper.xml : warning MSB3155: Item 'Microsoft.Net.Framework.3.5'
could not be located in 'c:\'.
  c:\mybootstrapper.xml : warning MSB3155: Item
'Microsoft.Windows.Installer.3.1' could not be located in 'c:\'.


"c:\mybootstrapper.xml" (default target) (1) ->
(Bootstrapper target) ->
  c:\mybootstrapper.xml(34,5): error MSB3147: Could not find required file
'setup.bin' in 'c:\Engine'.

    2 Warning(s)
    1 Error(s)

Time Elapsed 00:00:00.44

C:\Windows\Microsoft.NET\Framework64\v3.5>
------------

First of all, my build environment is Windows 7 based. So MSBuild does not
want to place the output in c:\ even though I belong to the administrator
group and this has been run from the command window which is running as an
administrator.

I then placed the bootstrapper.xml in the directory where I would like the
output to be placed.

This time it complained that it could not find the setup.bin in the \Engine
directory.

So I moved the bootstrapper file to the actual bootstrapper directory (i.e.
C:\Program Files (x86)\Microsoft SDKs\Windows\v7.0A\Bootstrapper) as MSBuild
seems to be looking for the setup.bin in the engine directory of off the
directory where bootstrapper.xml is located.

Now MSBuild complains that only one target can be handled in the switch. I
don't know what that means. It probably means that either Windows Installer
3.1 or Dot Net 3.5 can be bundled at one time but since DOt Net 3.5 requires
Windows Installler 3.1 I need to have both.
 
What is the purpose of running from
C:\Windows\Microsoft.NET\Framework64\v3.5 directory?

What is the mistake I am makng?

Thanks.

Umesh

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