diff --git a/src/lib/operations.test.ts b/src/lib/operations.test.ts
index ccb4ba288..985557be2 100644
--- a/src/lib/operations.test.ts
+++ b/src/lib/operations.test.ts
@@ -27,12 +27,31 @@ function userCall(name: string): Operation {
     sourceRange: defaultSourceRange(),
   }
 }
+
 function userReturn(): Operation {
   return {
     type: 'GroupEnd',
   }
 }
 
+function moduleBegin(name: string): Operation {
+  return {
+    type: 'GroupBegin',
+    group: {
+      type: 'ModuleInstance',
+      name,
+      moduleId: 0,
+    },
+    sourceRange: defaultSourceRange(),
+  }
+}
+
+function moduleEnd(): Operation {
+  return {
+    type: 'GroupEnd',
+  }
+}
+
 describe('operations filtering', () => {
   it('drops stdlib operations inside a user-defined function call', async () => {
     const operations = [
@@ -65,6 +84,25 @@ describe('operations filtering', () => {
     const actual = filterOperations(operations)
     expect(actual).toEqual([stdlib('std1'), stdlib('std2'), stdlib('std3')])
   })
+  it('does not drop module instances that contain no operations', async () => {
+    const operations = [
+      stdlib('std1'),
+      moduleBegin('foo'),
+      moduleEnd(),
+      stdlib('std2'),
+      moduleBegin('bar'),
+      moduleEnd(),
+      stdlib('std3'),
+    ]
+    const actual = filterOperations(operations)
+    expect(actual).toEqual([
+      stdlib('std1'),
+      moduleBegin('foo'),
+      stdlib('std2'),
+      moduleBegin('bar'),
+      stdlib('std3'),
+    ])
+  })
   it('preserves user-defined function calls at the end of the list', async () => {
     const operations = [stdlib('std1'), userCall('foo')]
     const actual = filterOperations(operations)
diff --git a/src/lib/operations.ts b/src/lib/operations.ts
index bb4e70d47..9d067c95a 100644
--- a/src/lib/operations.ts
+++ b/src/lib/operations.ts
@@ -1168,7 +1168,7 @@ export function filterOperations(operations: Operation[]): Operation[] {
  * for use in the feature tree UI
  */
 const operationFilters = [
-  isNotGroupWithNoOperations,
+  isNotUserFunctionWithNoOperations,
   isNotInsideGroup,
   isNotGroupEnd,
 ]
@@ -1202,22 +1202,28 @@ function isNotInsideGroup(operations: Operation[]): Operation[] {
 
 /**
  * A filter to exclude GroupBegin operations and their corresponding GroupEnd
- * that don't have any operations inside them from a list of operations.
+ * that don't have any operations inside them from a list of operations, if it's
+ * a function call.
  */
-function isNotGroupWithNoOperations(operations: Operation[]): Operation[] {
+function isNotUserFunctionWithNoOperations(
+  operations: Operation[]
+): Operation[] {
   return operations.filter((op, index) => {
     if (
       op.type === 'GroupBegin' &&
-      // If this is a begin at the end of the array, it's preserved.
+      op.group.type === 'FunctionCall' &&
+      // If this is a "begin" at the end of the array, it's preserved.
       index < operations.length - 1 &&
       operations[index + 1].type === 'GroupEnd'
     )
       return false
+    const previousOp = index > 0 ? operations[index - 1] : undefined
     if (
       op.type === 'GroupEnd' &&
-      // If this is an end at the beginning of the array, it's preserved.
-      index > 0 &&
-      operations[index - 1].type === 'GroupBegin'
+      // If this is an "end" at the beginning of the array, it's preserved.
+      previousOp !== undefined &&
+      previousOp.type === 'GroupBegin' &&
+      previousOp.group.type === 'FunctionCall'
     )
       return false