• Create uninstallSkype.xml file in the location where you have the Microsoft office package
• Edit uninstallSkype.xml file as given below, 
  <Configuration Product="LyncEntry"> 
  <Display Level="none" CompletionNotice="no" SuppressModal="yes" AcceptEula="yes" /> 
  <Setting Id="SETUP_REBOOT" Value="Never"/> 
  <Logging Path="C:\Skype"/>
  </Configuration>
• Save the filevafter making the customization changes. Note: Refer this document to know more about Microsoft Skype Product ID
• Create a package in Endpoint Central with MSIEXEC/EXE/ISS/Command as package type.
• Specify the UnInstallation Command with Switches/Arguments as setup.exe /uninstall LyncEntry /config uninstallSkype.xml
  For example, "\\DC-K12R2-1\DCSWRepository\SkypeForBusiness\setup.exe" /uninstall LyncEntry /config "\\DC-K12R2-1\DCSWRepository\SkypeForBusiness\uninstallSkype.xml"
• Click Add Package
• Create the configuration with the created package and deploy this to the target machine.

Steps to uninstall Skype for Business Basic 2016 Click-to-Run version:

• Download Office Deployment Tool and extract the files in a folder.
• Create a configuration file to uninstall Skype for Business Basic 2016 in the folder.

uninstallSkypeForBusiness.xml: 
//
<Configuration>
<Remove All="FALSE">
<Product ID="SkypeforBusinessEntryRetail" >
<Language ID="en-us" />
</Product>
</Remove>
<Display Level="None" AcceptEULA="TRUE"/>
</Configuration>
//

• Create package in Endpoint Central
• Upload setup.exe and uninstallSkypeForBusiness.xml using HTTP upload option.
• Use the below switch to uninstall the application
  setup.exe /configure uninstallSkypeForBusiness.xml
• If you want to uninstall using Network Path/HTTP Path, then paste the setup.exe and uninstallSkypeForBusiness.xml to the shared path and provide uninstall command as below:
  "\setup.exe" /configure "\uninstallSkypeForBusiness.xml"
• Create the configuration with the created package and deploy this to the target machine

Steps to remove Skype from Office 365:

• Download Office Deployment tool. Extract the downloaded files to a folder.
• Create uninstallSkype.xml file in the extracted office setup folder:

uninstallSkypeForBusiness.xml:
//
<Configuration>
<Add Version="MatchInstalled">
<Product ID="O365ProPlusRetail">
<Language ID="MatchOS" />
<ExcludeApp ID="Lync" />
</Product>
</Add>
<Display Level="None" AcceptEULA="TRUE" />
</Configuration> //
Note: If you are using Office 365 business edition, then the product ID should be O365BusinessRetail. The product ID may changed based on Office 365 edition used.

• Use the /download command to download all the dependant files.
• setup.exe /download uninstallSkype.xml
• Create Software Package in Endpoint Central. Zip the setup.exe, uninstallSkype.xml and the other downloaded Office files from this folder. Upload the zip files in the Endpoint Central package.
• Provide the silent switch as follows: setup.exe /configure uninstallSkype.xml
• If you want to uninstall using Network Path/HTTP Path, then paste the setup.exe and uninstallSkype.xml to sharepath and provide uninstall command as below: "<sharepath>\setup.exe" /configure "<sharepath>\uninstallSkype.xml"
• Deploy the package to the target machines. This will remove Skype For Business from the target machines. Note : Running this configuration will result in only Skype For Business exclusion.
• If you have excluded apps such as Groove or OneNote from the initial install, then you need to add them in the excluded apps list in uninstall xml.
• Kindly test this first before deploying it to the target machines.

How To's