diff --git a/middleman-core/features/clean_build.feature b/middleman-core/features/clean_build.feature
index fd8e1c4a..e5254df4 100644
--- a/middleman-core/features/clean_build.feature
+++ b/middleman-core/features/clean_build.feature
@@ -17,11 +17,28 @@ Feature: Build Clean
     And the file "build/index.html" should contain "Comment in layout"
 
   Scenario: Clean build an app with newly ignored files and a nested output directory
+    Given a fixture app "clean-nested-app"
+    When a file named "config.rb" with:
+      """
+      set :build_dir, "sub/dir"
+      """
     Given a built app at "clean-nested-app" with flags "--no-clean"
     Then a directory named "sub/dir" should exist
+    Then the following directories should exist:
+      | sub/dir                    |
+      | sub/dir/nested             |
     Then the following files should exist:
-      | sub/dir/about.html        |
-    When I append to "config.rb" with "ignore 'about.html'"
+      | sub/dir/about.html         |
+      | sub/dir/nested/nested.html |
+    When a file named "config.rb" with:
+      """
+      set :build_dir, "sub/dir"
+      ignore 'about.html'
+      ignore 'nested/*'
+      """
     Given a built app at "clean-nested-app"
+    Then the following directories should not exist:
+      | sub/dir/nested             |
     Then the following files should not exist:
-      | sub/dir/about.html        |
+      | sub/dir/about.html         |
+      | sub/dir/nested/nested.html |
diff --git a/middleman-core/fixtures/clean-nested-app/config.rb b/middleman-core/fixtures/clean-nested-app/config.rb
index de126643..e0438734 100644
--- a/middleman-core/fixtures/clean-nested-app/config.rb
+++ b/middleman-core/fixtures/clean-nested-app/config.rb
@@ -1,3 +1 @@
-set :build_dir, "sub/dir"
-
-
+set :build_dir, "sub/dir"
\ No newline at end of file
diff --git a/middleman-core/fixtures/clean-nested-app/source/nested/nested.html b/middleman-core/fixtures/clean-nested-app/source/nested/nested.html
new file mode 100644
index 00000000..40816a2b
--- /dev/null
+++ b/middleman-core/fixtures/clean-nested-app/source/nested/nested.html
@@ -0,0 +1 @@
+Hi
\ No newline at end of file
diff --git a/middleman-core/lib/middleman-core/cli/build.rb b/middleman-core/lib/middleman-core/cli/build.rb
index e068d3ac..a3261d2e 100644
--- a/middleman-core/lib/middleman-core/cli/build.rb
+++ b/middleman-core/lib/middleman-core/cli/build.rb
@@ -205,17 +205,14 @@ module Middleman::Cli
     # Remove files which were not built in this cycle
     # @return [void]
     def clean!
-      files       = @cleaning_queue.select { |q| q.file? }
-      directories = @cleaning_queue.select { |q| q.directory? }
-
-      files.each do |f|
+      @cleaning_queue.select { |q| q.file? }.each do |f|
         base.remove_file f, :force => true
       end
 
-      directories = directories.sort_by {|d| d.to_s.length }.reverse!
-
-      directories.each do |d|
-        base.remove_file d, :force => true if directory_empty? d
+      Dir[File.join(@destination, "**", "*")].select { |d|
+        File.directory?(d)
+      }.each do |d|
+        base.remove_file d, :force => true if directory_empty? Pathname(d)
       end
     end