Step 1: 

Extended Modules > Malaysia GST > Reports > Output tax Invoice Report or Input tax Invoice Report

Company: Select Company > Submit
Branch: Select ALL
Date: 2016 September filing cycle
Document Type: Select All
After generate the report > Click "Export CSV"

Step 2:

Select Row 1 > Click "Filter" 
Filter for ZRE tax code > select "0"
copy the information to new "sheet", 
then sum up all column 
the " Supply Value MYR" same with GST-03: 11 

Step 3: (IF ANY)

Repeat for Step 2 for ES43
GST-03: 12 

Step 4:

Select Row 1 > Click "Filter" 
Filter for SR tax code > Deselect "Blank"
copy the information to new "sheet", 
then sum up all column 
the " Supply Value MYR" same with GST-03: 5a
the " GST Value" same with GST-03: 5b

Related WIKI Page: