Step 1: Make sure you have received an intimation under section 143 (1) from CPC Bangalore for the E-returns filed by you for AY 2009-10 or later.
Step 2: Carefully examine the intimation to see if the computation by CPC is correct even if different from what was expected by you. It may be that you may have computed tax liability or interest incorrectly.
Step 3: Carefully review the Common Error guide and the table above to understand as the basic reason for the variation.
Step 4: Since the Rectification Request is to be submitted by uploading the complete xml file similar to uploading the original return, it may be preferable to start with the saved e-return data that was prepared by the return preparation utility/software (Department provided excel software or other software), in case it is available with the taxpayer.
Step 5: All errors in data entry should be completely corrected and schedules or fields left blank should be filled accurately as explained in the guide. The complete return should be filled including TDS and Tax payment schedules and not only schedules that need change or the fields that need correction. This is because the entire return with corrected data would be re-processed under rectification.
However, there should not be any revision in income figures or new claims since then the rectification request would be rejected or rectification would be delayed. It may be clearly noted that this facility is only for correcting mistakes apparent from record.
Step 6: After the Return data is corrected then the xml can be generated. This is the Rectification XML file.
Step 7: Log in to http://incometaxindiaefiling.gov.in and go to My Account-> Rectification-> Rectification upload
Step 8: Fill in details from the intimation sheet which will be verified to ascertain that only the taxpayer in possession of the Intimation from CPC would be able to submit a rectification request.
Step 9: Fill in details of Schedules where changes have been made and reasons for seeking rectification.
Fill in due date for filing return, if incorrect as per intimation sheet. Leave blank if not applicable.
Fill in details which are not available in the return form such as details of 80G donations (not available in ITR forms for 1, 2 and 3) and Quarter-wise details of Capital Gains (all four types- which is not available in ITRs 2, 3, 4, 5 and 6 for AY 2009-10) only if applicable. Leave blank if not applicable
Please note if your address has been changed in the rectification XML file, you should check the address changed checkbox to ensure that the new address is updated else the old address as per e-return only will be used.
Step 10: Now upload the Rectification XML file. Validations will be done to ascertain that only mistakes apparent from record are sought to be rectified
Step 11: Upon successful upload, Rectification Request number and acknowledgement will be displayed.
In case Bank Account Number is changed in rectification XML as compared to Bank Account number as per e-return then the rectification request is only PROVISIONALLY uploaded. A response sheet will be displayed, which has to be filled and a cancelled cheque attached and sent to CPC Bangalore. Only upon receipt of this response sheet at CPC Bangalore will the Rectification Request be finally accepted and acknowledgement generated.
Step 12: The rectification request can be withdrawn within 7 days if uploaded by mistake or the request needed to be amended. Only one rectification request can be submitted at any time. Any rectification request after submission has to be processed at CPC before the next rectification request for the same PAN and AY can be submitted.
Step 13: The rectification request will be processed at CPC and either the rectification order under Section 154 will be issued or the request would be rejected.

Please refer the document How to Rectify Online Income Tax Returns in response to Intimation U/S 143(1)