As has been mentioned; if you want to sell particular shares then you need to keep a spreadsheet
After the sale you need to go into 'portfolio' click edit and change the cost of your shares
For example
Buy 1000 at 50c Buy 1000 at $1 Buy 1000 at $1.5
CommSec will show 3000 at a cost of $3000 ie $1 each
If you sold the 1000 parcel of $1.50 shares, CommSec will show 2000 shares at an ave cost of $1 ie $2000
In reality, the cost of your remaining 2000 shares is $1500 ie 75 cents
So, go into portfolio and change the cost from $1 to 75 cents
CommSec can only average as they don't know which particular shares you are selling
Unless you are going to use ave cost you must keep a detailed spreadsheet to record which particular shares you are selling so that you can work out your profit/loss for each sale
