diff --git a/config.example.toml b/config.example.toml
index 4a7578e..50806ef 100644
--- a/config.example.toml
+++ b/config.example.toml
@@ -1,6 +1,7 @@
 [files]
 input_path = "/data/input"
 output_path = "/data/output"
+keep_directory_structure = true # keep directory structure when outputting files
 include = [ 'mp4', 'avi', 'mkv' ] # file extensions to include
 
 [files.cleanup]
diff --git a/src/configuration/mod.rs b/src/configuration/mod.rs
index 04a2131..e7eab65 100644
--- a/src/configuration/mod.rs
+++ b/src/configuration/mod.rs
@@ -32,6 +32,7 @@ pub struct ConfigFilesCleanup {
 pub struct ConfigFiles {
     pub input_path: String,
     pub output_path: String,
+    pub keep_directory_structure: Option<bool>,
     pub include: Vec<String>,
     pub cleanup: Option<ConfigFilesCleanup>,
 }
@@ -51,6 +52,7 @@ impl Config {
             files: ConfigFiles {
                 input_path: String::from("/data/input"),
                 output_path: String::from("/data/output"),
+                keep_directory_structure: None,
                 include: Vec::new(),
                 cleanup: None,
             },
diff --git a/src/main.rs b/src/main.rs
index 05dd769..eeff7cd 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -47,9 +47,21 @@ fn start_transcode_run(input_files: &Vec<PathBuf>, config: &Config) -> i32 {
             error!("Failed to process file {}: {}", job.input, remarks);
         };
 
-        let mut output_path = file.clone();
+        let mut output_path = if let Some(keep_directory_structure) = config.files.keep_directory_structure {
+            if keep_directory_structure {
+                let mut output_path = PathBuf::from(&config.files.output_path);
+                output_path.push(file.strip_prefix(&config.files.input_path).unwrap());
+                output_path
+            } else {
+                PathBuf::from(&config.files.output_path)
+                    .join(file.file_name().unwrap())
+            }
+        } else {
+            PathBuf::from(&config.files.output_path)
+                .join(file.file_name().unwrap())
+        };
         output_path.set_extension(&config.ffmpeg.output.format);
-        let output_path = PathBuf::from(&config.files.output_path).join(output_path.file_name().unwrap()); // TODO: This is a bit of a mess.
+
 
         let job = TranscodeJob::new(
             file.to_str().unwrap(),
@@ -87,7 +99,27 @@ fn start_transcode_run(input_files: &Vec<PathBuf>, config: &Config) -> i32 {
             continue;
         }
 
-        // TODO: Cleanup
+        if let Some(cleanup) = &config.files.cleanup {
+            if !cleanup.enabled { () }
+            match cleanup.original_cleanup_behavior {
+                configuration::ConfigFilesCleanupOriginalBehavior::delete => {
+                    if let Err(e) = std::fs::remove_file(&job.input) {
+                        error!("Failed to delete original file {}: {}", job.input, e);
+                    }
+                },
+                configuration::ConfigFilesCleanupOriginalBehavior::archive => {
+                    let mut archive_path = PathBuf::from(&cleanup.archive.path);
+                    archive_path.push(job.input.strip_prefix(&config.files.input_path).unwrap());
+                    if let Err(e) = std::fs::create_dir_all(archive_path.parent().unwrap()) {
+                        error!("Failed to create archive directory {}: {}", archive_path.parent().unwrap().to_str().unwrap(), e);
+                    }
+                    if let Err(e) = std::fs::rename(&job.input, &archive_path) {
+                        error!("Failed to archive original file {}: {}", job.input, e);
+                    }
+                },
+                configuration::ConfigFilesCleanupOriginalBehavior::keep => (),
+            }
+        }
 
         info!("Finished processing file {}.", job.input);
         success_count += 1;