diff --git a/src/obicompactvec/src/bitmatrix.rs b/src/obicompactvec/src/bitmatrix.rs
index ead53af..5fd426b 100644
--- a/src/obicompactvec/src/bitmatrix.rs
+++ b/src/obicompactvec/src/bitmatrix.rs
@@ -190,6 +190,10 @@ pub fn pack_bit_matrix(dir: &Path) -> io::Result<()> {
     file.write_all(&(n_cols as u64).to_le_bytes())?;
     for &off in &offsets { file.write_all(&off.to_le_bytes())?; }
     for data in &col_files { file.write_all(data)?; }
+    drop(file);
+
+    for c in 0..n_cols { fs::remove_file(col_path(dir, c))?; }
+    fs::remove_file(dir.join("meta.json"))?;
     Ok(())
 }
 
diff --git a/src/obicompactvec/src/intmatrix.rs b/src/obicompactvec/src/intmatrix.rs
index 5fa1cc4..d1421e5 100644
--- a/src/obicompactvec/src/intmatrix.rs
+++ b/src/obicompactvec/src/intmatrix.rs
@@ -293,6 +293,10 @@ pub fn pack_compact_int_matrix(dir: &Path) -> io::Result<()> {
     file.write_all(&(n_cols as u64).to_le_bytes())?;
     for &off in &offsets { file.write_all(&off.to_le_bytes())?; }
     for data in &col_files { file.write_all(data)?; }
+    drop(file);
+
+    for c in 0..n_cols { fs::remove_file(col_path(dir, c))?; }
+    fs::remove_file(dir.join("meta.json"))?;
     Ok(())
 }
 
diff --git a/src/obikindex/src/rebuild.rs b/src/obikindex/src/rebuild.rs
index 95dc4b8..c7ac4fd 100644
--- a/src/obikindex/src/rebuild.rs
+++ b/src/obikindex/src/rebuild.rs
@@ -112,6 +112,8 @@ impl KmerIndex {
         // Write SENTINEL_INDEXED — output is ready to use.
         fs::File::create(output.join(SENTINEL_INDEXED))?;
 
-        KmerIndex::open(output)
+        let idx = KmerIndex::open(output)?;
+        idx.pack_matrices()?;
+        Ok(idx)
     }
 }