How can a subfeature of a program be uninstalled using msiexec ?

Define 'subfeature'.  afaik Installer software can only uninstall files or merge modules.

This will depend on how you have created the installation package.

You have components and features.

Each component has a set of "items" that are part of it (files/registry settings/etc).
Components are then grouped under features.

It is possible to have sub-features :
Feature : XP Install
Sub-feature : System has Application : BLAH
Sub-Feature: System has Application : BLEAH

I would reccomend installing the platform SDK (including the windows installer sdk) and then looking through the documentation, a link to a part about this when you have the SDK installed is :
ms-help://MS.PSDKSVR2003SP1.1033/msi/setup/working_with_features_and_components.htm

The command line interface for msiexec won't help you here, the link below shows all of the possible parameters :
http://www.microsoft.com/resources/documentation/windows/xp/all/proddocs/en-us/msiexec.mspx?mfr=true

The one way you can do this is to create a transform that removes what you are looking for and "apply" that transform to the installation.