I heard that STM32 doesn't requires any JTAG for uploading bootloader since it have builtin bootloader.
No Arduino requires JTAG.
Can I able to convert the arduino program to .hex format?
I am not sure you understand what you are saying. True .hex is a file format but that is all it is, the contents are not specified. When you compile source code you can store the resultant machine code in a .hex file, but this is different code depending on the target processor.
Now I planned to buy a STM32F1xx series of 32 bit MCU
What Arduino is this? If it is not supported by the Arduino IDE then you won't be able to use it.