diff --git a/build.sh b/build.sh
index 603da10..1456303 100755
--- a/build.sh
+++ b/build.sh
@@ -36,8 +36,8 @@ setup_temp_dir() {
 }
 
 setup_output_dir() {
-	rm -r output # Delete existing 'output' directory
-	cp -r source output #Copy directory structure from 'source' to 'output'
+	rm -r "${BASE_PATH}/output" # Delete existing 'output' directory
+	cp -r "${BASE_PATH}/source" "${BASE_PATH}/output" #Copy directory structure from 'source' to 'output'
 }
 
 del_files_in_output() {
@@ -96,12 +96,17 @@ md_to_html() {
 		let num_lines=$(echo $metadata | wc -l)+1
 		sed -i "1,${num_lines}d" $BASE_PATH/temp/`basename $file`
 
-		pandoc -f markdown $BASE_PATH/temp/`basename $file` > $BASE_PATH/output/`basename $file .md`.html
+#		Construct path for output file
+		path_for_output=$(realpath --relative-to="${BASE_PATH}/source" $file)
+		path_for_output="${BASE_PATH}/output/${path_for_output}"
+		path_for_output="$(dirname $path_for_output)/$(basename $path_for_output .md).html"
+
+#		Convert the file, and place the output in the correct location
+		pandoc -f markdown $BASE_PATH/temp/`basename $file` > ${path_for_output}
 		rm $BASE_PATH/temp/*
-		html_file="$BASE_PATH/output/`basename $file .md`.html"
 
-		add_header_and_footer $html_file
-		replace_vars $html_file #Uses 'meta_key' and 'meta_value' arrays
+		add_header_and_footer $path_for_output
+		replace_vars $path_for_output #Uses 'meta_key' and 'meta_value' arrays
 
 		unset metadata meta_key meta_value
 	done