I want my linux system to act as a peripheral device which is advertising some data in the bluetooth LE communication. Can I use the android apps like ble scanner or ble explorer to check whether my system is advertising successfully?
Absolutely, I certainly have.
I recommend the Bleno node.js module for advertising on your Linux box. And for Android I've used Nordic's nRF Master Control Panel or simply build the Android sample BluetoothLeGatt app to scan for an check on the services offered by your Linux box.