I just thought i needed to reiterate the issue for better clarity:

Below is the directory structure in my source .wxs file:
  <Directory Id='TARGETDIR' Name='SourceDir'>
       <Directory Id='EnergySolutionsConfig' Name="Energy Solution 
International">
        <Directory Id='PFWServiceFolder' Name="PFWService">
          <Directory Id='CONFIG' Name="config">
            <Component Id="x86RegEntPFWConfig" 
Guid="5DAD9B46-43BB-42D2-91E9-F2248369AA68" Win64="no">
              <RegistryValue Id="x86PFWConfigRegValue" Root="HKLM" 
Key="SOFTWARE\[Manufacturer]" Name="ConfigPath" Value="[CONFIG]"
                 Type="string" />
            </Component>
            <Component Id="x64RegEntPFWConfig" 
Guid="57240178-4A44-4C6F-A11C-B4DE99573DE0" Win64="yes">
              <RegistryValue Id="x64PFWConfigRegValue" Root="HKLM" 
Key="SOFTWARE\[Manufacturer]" Name="ConfigPath" Value="[CONFIG]"
                 Type="string" />
            </Component>
          </Directory>
          </Directory>
       </Directory>
     </Directory>

The heat harvests directories from a location D:\Configrelease which has 
directories such as "command_processors". The produces config.wxs file 
that has below structure:
<Fragment>
         <DirectoryRef Id="CONFIG">
             <Component Id="cmpC405575C36944E434C00DCE528FA79EA" 
Guid="{0EDAF860-B5C3-4C93-BDD7-EB1947D94749}">
                 <File Id="fil62BA9BFC68F4D3C2DE913D9ABFEDC429" 
KeyPath="yes" Source="$(var.ConfigPath)\PFWConfiguration.xml" />
             </Component>
             <Directory Id="dirB9FCE785B12AD5549EC71DC5DC66ED48" 
Name="archives">

             </Directory>
             <Directory Id="dirB8C0CFD798C8A57234B0C04A4E266B86" 
Name="command_processors">
                 <Component Id="cmpE03A5A54FF75ABF0FA6DA591BC4F3152" 
Guid="{F2158D98-1DC2-4348-89FC-65A2115084B6}" KeyPath="yes">
                     <CreateFolder />
                 </Component>

After i run the installer, i browse to "C:\Energy Solutions 
International\PFWService\config\command_processors" and keep this path 
open, and then uninstall the directory structure that does not get 
removed is "C:\Energy Solutions International\PFWService".

Is it because of the <CreateFolder> in the config.wxs(as Wesley had 
suggest) file that heat creates that i am facing this issue. If so what 
is the way out. Hope i have explained the situation better this time, 
apologies if i created any confusion.

Regards,
SuvraJyoti

On 17-12-2013 14:27, Suvrajyoti Panda wrote:
> Hey Blair,
>
> The scenario you have mentioned in the first para of your response is
> exactly what is happening. So is there no way that we can handle the
> folder removal on uninstall even if that path is open, or this is a
> known issue?
>
> Regards,
> SuvraJyoti
> On 17-12-2013 14:14, Blair Murri wrote:
>> If a file being removed can’t be moved, then it will be marked for removal 
>> during reboot, and unfortunately the folder will then be left behind 
>> (because only file delete records are placed into the reboot sequence, not 
>> folders). After reboot there isn’t an installation left to run to cleanup 
>> any further.
>>
>>
>> Most of the time, files still in use can be moved (even if they are still 
>> loaded in other processes) and the folder is thus removed during the 
>> installation transaction (before the reboot) and the moved file is then 
>> removed as part of the reboot sequence.
>>
>>
>>
>>
>>
>>
>> -Blair
>>
>>
>>
>>
>>
>> From: Suvrajyoti Panda
>> Sent: ‎Monday‎, ‎December‎ ‎16‎, ‎2013 ‎8‎:‎57‎ ‎PM
>> To: General discussion for Windows Installer XML toolset.
>>
>>
>>
>>
>>
>> No Wesley, I have not used any create folder over here.
>>
>> Regards,
>> SuvraJyoti
>>
>> On 16-12-2013 20:03, Wesley Manning wrote:
>>> Did you use CreateFolder to create this directory?  If so I think you need 
>>> to use RemoveFolder to remove the folder.  Not sure about that though.
>>>
>>> -----Original Message-----
>>> From: Suvrajyoti Panda [mailto:suvrajyo...@contata.co.in]
>>> Sent: December-16-13 12:37 AM
>>> To: General discussion about the WiX toolset.
>>> Subject: Re: [WiX-users] Uninstall by Installer not removing the path 
>>> created if that path is open on the system
>>>
>>> Hey Wesley,
>>>
>>> checked it on a reboot, that does not work. The structure is still there. 
>>> Any others suggestions guys?
>>>
>>> Regards,
>>> SuvraJyoti
>>> On 13-12-2013 20:13, Wesley Manning wrote:
>>>> It might be removed on a reboot.  If you had folder open, then windows 
>>>> installer can't uninstall it.  But I think it marks it for removal.  I 
>>>> know for sure files have this behaviour but I'm not sure about folders.
>>>>
>>>> -----Original Message-----
>>>> From: Suvrajyoti Panda [mailto:suvrajyo...@contata.co.in]
>>>> Sent: December-13-13 1:48 AM
>>>> To: General discussion about the WiX toolset.
>>>> Subject: [WiX-users] Uninstall by Installer not removing the path
>>>> created if that path is open on the system
>>>>
>>>> Hi All,
>>>>
>>>> I just saw this behaviour. My installer creates the following :"C:\Energy 
>>>> Solutions International\PFWService\config", if this path is open and i run 
>>>> the uninstall from control panel, then the path remains("C:\Energy 
>>>> Solutions International\PFWService\config") although files under it is 
>>>> removed. Is it expected behavior or incorrect. If incorrect what is the 
>>>> workaround for the same.
>>>>
>>>> Regards,
>>>> SuvraJyoti
>>>>
>>>> ----------------------------------------------------------------------
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>> mNo
>>
>> ------------------------------------------------------------------------------
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>> organizations don't have a clear picture of how application performance
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>> ------------------------------------------------------------------------------
>> Rapidly troubleshoot problems before they affect your business. Most IT
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>
> ------------------------------------------------------------------------------
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> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
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