diff --git a/lib/brakeman.rb b/lib/brakeman.rb
index b2edc4bb0d..fc91f3b31f 100644
--- a/lib/brakeman.rb
+++ b/lib/brakeman.rb
@@ -556,7 +556,7 @@ def self.filter_warnings tracker, options
 
     if options[:interactive_ignore]
       require 'brakeman/report/ignore/interactive'
-      config = InteractiveIgnorer.new(file, tracker.warnings).start
+      config = InteractiveIgnorer.new(app_tree, file, tracker.warnings).start
     else
       notify "[Notice] Using '#{file}' to filter warnings"
       config = IgnoreConfig.new(file, tracker.warnings)
diff --git a/lib/brakeman/file_path.rb b/lib/brakeman/file_path.rb
index 05a6a318cb..a4cedc2cb9 100644
--- a/lib/brakeman/file_path.rb
+++ b/lib/brakeman/file_path.rb
@@ -50,6 +50,10 @@ def exists?
       File.exist? self.absolute
     end
 
+    def empty?
+      self.relative.to_s.empty?
+    end
+
     # Compare FilePaths. Raises an ArgumentError unless both objects are FilePaths.
     def <=> rhs
       raise ArgumentError unless rhs.is_a? Brakeman::FilePath
diff --git a/lib/brakeman/report/ignore/interactive.rb b/lib/brakeman/report/ignore/interactive.rb
index 81ce04a1dc..0e6799d6f8 100644
--- a/lib/brakeman/report/ignore/interactive.rb
+++ b/lib/brakeman/report/ignore/interactive.rb
@@ -2,7 +2,7 @@
 
 module Brakeman
   class InteractiveIgnorer
-    def initialize file, warnings
+    def initialize app_tree, file, warnings
       @ignore_config = Brakeman::IgnoreConfig.new(file, warnings)
       @new_warnings = warnings
       @skip_ignored = false
@@ -10,6 +10,7 @@ def initialize file, warnings
       @ignore_rest = false
       @quit = false
       @restart = false
+      @app_tree = app_tree
     end
 
     def start
@@ -35,15 +36,17 @@ def start
 
     def file_menu
       loop do
-        @ignore_config.file = HighLine.new.ask "Input file: " do |q|
+        input_file = HighLine.new.ask "Input file: " do |q|
           if @ignore_config.file and not @ignore_config.file.empty?
-            q.default = @ignore_config.file
+            q.default = @ignore_config.file.relative
           else
             q.default = "config/brakeman.ignore"
           end
         end
 
-        if File.exist? @ignore_config.file
+        @ignore_config.file = Brakeman::FilePath.from_app_tree(@app_tree, input_file)
+
+        if @ignore_config.file && @ignore_config.file.exists?
           @ignore_config.read_from_file
           return
         else
@@ -168,14 +171,16 @@ def final_menu
     end
 
     def save
-      @ignore_config.file = HighLine.new.ask "Output file: " do |q|
+      output_file = HighLine.new.ask "Output file: " do |q|
         if @ignore_config.file and not @ignore_config.file.empty?
-          q.default = @ignore_config.file
+          q.default = @ignore_config.file.relative
         else
           q.default = "config/brakeman.ignore"
         end
       end
 
+      @ignore_config.file = Brakeman::FilePath.from_app_tree(@app_tree, output_file)
+
       @ignore_config.save_with_old
     end
 
diff --git a/test/tests/file_path.rb b/test/tests/file_path.rb
index 80cfbdce9a..6335202b9b 100644
--- a/test/tests/file_path.rb
+++ b/test/tests/file_path.rb
@@ -43,6 +43,17 @@ def test_file_path_to_str
     assert_equal "/tmp/blah/thing.rb", "#{fp}"
   end
 
+  def test_file_path_empty?
+    at = Brakeman::AppTree.new("/tmp/blah")
+    fp1 = Brakeman::FilePath.from_app_tree at, "/tmp/blah/thing.rb"
+    fp2 = Brakeman::FilePath.from_app_tree at, "/tmp/blah/thing/"
+    fp3 = Brakeman::FilePath.from_app_tree at, ""
+
+    refute fp1.empty?
+    refute fp2.empty?
+    assert fp3.empty?
+  end
+
   def test_file_path_equality
     at = Brakeman::AppTree.new("/tmp/blah")
     fp1 = Brakeman::FilePath.from_app_tree at, "/tmp/blah/thing.rb"