diff --git a/src/ALZ/Private/Deploy-Accelerator-Helpers/New-Bootstrap.ps1 b/src/ALZ/Private/Deploy-Accelerator-Helpers/New-Bootstrap.ps1
index e52203a..157cee4 100644
--- a/src/ALZ/Private/Deploy-Accelerator-Helpers/New-Bootstrap.ps1
+++ b/src/ALZ/Private/Deploy-Accelerator-Helpers/New-Bootstrap.ps1
@@ -66,15 +66,42 @@ function New-Bootstrap {
 
         # Get starter module
         $starterModulePath = ""
+        $starterRootModuleFolder = ""
+        $starterRootModuleFolderPath = ""
+        $starterFoldersToRetain = @()
 
         if($hasStarter) {
             if($inputConfig.starter_module_name -eq "") {
                 $inputConfig.starter_module_name = Request-SpecialInput -type "starter" -starterConfig $starterConfig
             }
 
+            $chosenStarterConfig = $starterConfig.starter_modules.$($inputConfig.starter_module_name)
+
             Write-Verbose "Selected Starter: $($inputConfig.starter_module_name))"
-            $starterModulePath = (Resolve-Path (Join-Path -Path $starterPath -ChildPath $starterConfig.starter_modules.$($inputConfig.starter_module_name).location)).Path
+            $starterModulePath = (Resolve-Path (Join-Path -Path $starterPath -ChildPath $chosenStarterConfig.location)).Path
+            $starterRootModuleFolderPath = $starterModulePath
             Write-Verbose "Starter Module Path: $starterModulePath"
+
+            if($chosenStarterConfig.PSObject.Properties.Name -contains "additional_retained_folders") {
+                $starterFoldersToRetain = $chosenStarterConfig.additional_retained_folders
+                Write-Verbose "Starter Additional folders to retain: $($starterFoldersToRetain -join ",")"
+            }
+
+            if($chosenStarterConfig.PSObject.Properties.Name -contains "root_module_folder") {
+                $starterRootModuleFolder = $chosenStarterConfig.root_module_folder
+
+                # Retain the root module folder
+                $starterFoldersToRetain += $starterRootModuleFolder
+
+                # Add the root module folder to bootstrap input config
+                $inputConfig | Add-Member -NotePropertyName "root_module_folder_relative_path" -NotePropertyValue $starterRootModuleFolder
+
+                # Set the starter root module folder full path
+                $starterRootModuleFolderPath = Join-Path -Path $starterModulePath -ChildPath $starterRootModuleFolder
+
+                Write-Verbose "Starter root module folder: $starterRootModuleFolder"
+                Write-Verbose "Starter final folders to retain: $($starterFoldersToRetain -join ",")"
+            }
         }
 
         # Getting configuration for the bootstrap module user input
@@ -92,7 +119,7 @@ function New-Bootstrap {
         if($hasStarter) {
             Write-Verbose "Getting the starter configuration..."
             if($iac -eq "terraform") {
-                $terraformFiles = Get-ChildItem -Path $starterModulePath -Filter "*.tf" -File
+                $terraformFiles = Get-ChildItem -Path $starterRootModuleFolderPath -Filter "*.tf" -File
                 foreach($terraformFile in $terraformFiles) {
                     $starterParameters = Convert-HCLVariablesToInputConfig -targetVariableFile $terraformFile.FullName -hclParserToolPath $hclParserToolPath -validators $validationConfig -appendToObject $starterParameters
                 }
@@ -140,13 +167,26 @@ function New-Bootstrap {
         # Creating the tfvars files for the bootstrap and starter module
         $tfVarsFileName = "terraform.tfvars.json"
         $bootstrapTfvarsPath = Join-Path -Path $bootstrapModulePath -ChildPath $tfVarsFileName
-        $starterTfvarsPath = Join-Path -Path $starterModulePath -ChildPath "terraform.tfvars.json"
+        $starterTfvarsPath = Join-Path -Path $starterRootModuleFolderPath -ChildPath "terraform.tfvars.json"
         $starterBicepVarsPath = Join-Path -Path $starterModulePath -ChildPath "parameters.json"
 
         # Write the tfvars file for the bootstrap and starter module
         Write-TfvarsJsonFile -tfvarsFilePath $bootstrapTfvarsPath -configuration $bootstrapConfiguration
 
         if($iac -eq "terraform") {
+            if($starterFoldersToRetain.Length -gt 0) {
+                Write-Verbose "Removing unwanted folders from the starter module..."
+                $folders = Get-ChildItem -Path $starterModulePath -Directory
+                foreach($folder in $folders) {
+                    if($starterFoldersToRetain -notcontains $folder.Name) {
+                        Write-Verbose "Removing folder: $($folder.FullName)"
+                        Remove-Item -Path $folder.FullName -Recurse -Force
+                    } else {
+                        Write-Verbose "Retaining folder: $($folder.FullName)"
+                        Remove-TerraformMetaFileSet -path $folder.FullName -writeVerboseLogs:$writeVerboseLogs.IsPresent
+                    }
+                }
+            }
             Remove-TerraformMetaFileSet -path $starterModulePath -writeVerboseLogs:$writeVerboseLogs.IsPresent
             Write-TfvarsJsonFile -tfvarsFilePath $starterTfvarsPath -configuration $starterConfiguration
         }