diff --git a/pyzebra/ccl_process.py b/pyzebra/ccl_process.py
index 9ef8cd4..6ba08f6 100644
--- a/pyzebra/ccl_process.py
+++ b/pyzebra/ccl_process.py
@@ -99,30 +99,39 @@ def merge_scans(scan_into, scan_from):
 
     scan_motor = scan_into["scan_motor"]  # the same as scan_from["scan_motor"]
 
-    if (
-        scan_into[scan_motor].shape == scan_from[scan_motor].shape
-        and np.max(np.abs(scan_into[scan_motor] - scan_from[scan_motor])) < 0.0005
-    ):
-        counts_tmp = 0
-        counts_err_tmp = 0
+    pos_all = np.array([])
+    val_all = np.array([])
+    err_all = np.array([])
+    for scan in [scan_into["init_scan"], *scan_into["merged_scans"]]:
+        pos_all = np.append(pos_all, scan[scan_motor])
+        val_all = np.append(val_all, scan["counts"])
+        err_all = np.append(err_all, scan["counts_err"] ** 2)
 
-        for scan in [scan_into["init_scan"], *scan_into["merged_scans"]]:
-            counts_tmp += scan["counts"]
-            counts_err_tmp += scan["counts_err"] ** 2
+    sort_index = np.argsort(pos_all)
+    pos_all = pos_all[sort_index]
+    val_all = val_all[sort_index]
+    err_all = err_all[sort_index]
 
-        scan_into["counts"] = counts_tmp / (1 + len(scan_into["merged_scans"]))
-        scan_into["counts_err"] = np.sqrt(counts_err_tmp)
+    pos_tmp = pos_all[:1]
+    val_tmp = val_all[:1]
+    err_tmp = err_all[:1]
+    num_tmp = np.array([1])
+    for pos, val, err in zip(pos_all[1:], val_all[1:], err_all[1:]):
+        if pos - pos_tmp[-1] < 0.0005:
+            # the repeated motor position
+            val_tmp[-1] += val
+            err_tmp[-1] += err
+            num_tmp[-1] += 1
+        else:
+            # a new motor position
+            pos_tmp = np.append(pos_tmp, pos)
+            val_tmp = np.append(val_tmp, val)
+            err_tmp = np.append(err_tmp, err)
+            num_tmp = np.append(num_tmp, 1)
 
-    else:
-        motor_pos = np.concatenate((scan_into[scan_motor], scan_from[scan_motor]))
-        counts = np.concatenate((scan_into["counts"], scan_from["counts"]))
-        counts_err = np.concatenate((scan_into["counts_err"], scan_from["counts_err"]))
-
-        index = np.argsort(motor_pos)
-
-        scan_into[scan_motor] = motor_pos[index]
-        scan_into["counts"] = counts[index]
-        scan_into["counts_err"] = counts_err[index]
+    scan_into[scan_motor] = pos_tmp
+    scan_into["counts"] = val_tmp / num_tmp
+    scan_into["counts_err"] = np.sqrt(err_tmp)
 
     scan_from["export"] = False