diff --git a/src/filterColumns.ts b/src/filterColumns.ts
index aec6b0a..f2ba59c 100644
--- a/src/filterColumns.ts
+++ b/src/filterColumns.ts
@@ -1,12 +1,30 @@
 import { CsvTable } from './loadCsv.models';
 
-const filterColumns = (table: CsvTable, columnNames: string[]) => {
-  const indexKeepDecisions = table[0].map(
-    (header) => columnNames.indexOf(header as string) > -1
+/**
+ * Filters and re-orders columns in a given CSV table.
+ *
+ * Where n is the number of non-header cells in `table`, `m` is the number of header cells in `table`, and h is the number of items in `headers`
+ *
+ * Time complexity: O(n + mh)
+ *
+ * Space complexity: O(n + m + h)
+ */
+const filterColumns = (table: CsvTable, headers: string[]) => {
+  const indexKeepDecisions = table[0].map((columnName) =>
+    headers.includes(columnName as string)
   );
-  return table.map((row) =>
-    row.filter((_, index) => indexKeepDecisions[index])
+  const filteredColumnNames = table[0].filter((_, i) => indexKeepDecisions[i]);
+  const indexMap = filteredColumnNames.map((columnName) =>
+    headers.indexOf(columnName as string)
   );
+  return table.map((row) => {
+    const newRow = new Array(indexMap.length);
+    for (let i = 0, j = 0; i < row.length; i++) {
+      if (!indexKeepDecisions[i]) continue;
+      newRow[indexMap[j++]] = row[i];
+    }
+    return newRow;
+  });
 };
 
 export default filterColumns;
diff --git a/src/loadCsv.ts b/src/loadCsv.ts
index aa7a0fe..0db7cd8 100644
--- a/src/loadCsv.ts
+++ b/src/loadCsv.ts
@@ -45,8 +45,6 @@ const loadCsv = (
     throw new Error('CSV file can not be shorter than two rows');
   }
 
-  applyMappings(data, mappings, new Set(flatten));
-
   const tables: { [key: string]: CsvTable } = {
     labels: filterColumns(data, labelColumns),
     features: filterColumns(data, featureColumns),
@@ -54,6 +52,11 @@ const loadCsv = (
     testLabels: [],
   };
 
+  const flattenSet = new Set(flatten);
+
+  applyMappings(tables.labels, mappings, flattenSet);
+  applyMappings(tables.features, mappings, flattenSet);
+
   tables.labels.shift();
   const featureColumnNames = tables.features.shift() as string[];
 
diff --git a/tests/filterColumns.test.ts b/tests/filterColumns.test.ts
index a92de95..c3999e8 100644
--- a/tests/filterColumns.test.ts
+++ b/tests/filterColumns.test.ts
@@ -2,8 +2,8 @@ import filterColumns from '../src/filterColumns';
 
 const data = [
   ['lat', 'lng', 'country'],
-  ['0.234', '1.47', 'SomeCountria'],
-  ['-293.2', '103.34', 'SomeOtherCountria'],
+  ['0', '1.47', 'SomeCountria'],
+  ['1', '103.34', 'SomeOtherCountria'],
 ];
 
 test('Filtering a single column works correctly', () => {
@@ -11,11 +11,11 @@ test('Filtering a single column works correctly', () => {
   expect(result).toMatchObject([['lng'], ['1.47'], ['103.34']]);
 });
 
-test('Filtering multiple columns works correctly', () => {
-  const result = filterColumns(data, ['country', 'lng']); // Column order from the CSV should be preserved.
+test('Filtering multiple columns works correctly, respects order in second argument, does not break with multiple same name columns', () => {
+  const result = filterColumns(data, ['country', 'lat']); // Column order from the CSV should be preserved.
   expect(result).toMatchObject([
-    ['lng', 'country'],
-    ['1.47', 'SomeCountria'],
-    ['103.34', 'SomeOtherCountria'],
+    ['country', 'lat'],
+    ['SomeCountria', '0'],
+    ['SomeOtherCountria', '1'],
   ]);
 });