How to make final good looking prototype of our project?
First, get your circuit mounted in a permanent configuration.  It doesn't have to be beautiful, but it can't have connections that go intermittent because of mechanical issues.  Solderless breadboards are a non-starter here, regardless of how much they helped (or hindered) you during earlier development stages.  There are through-hole prototype boards, mostly with 0.1" patterns, with and without busses, that are great for through hole parts.

from www.netams.com/~anton/usb-adc/08310001.jpg

If you have SMD parts, you either need to have a PCB made or you can use a board that breaks out the SMD part into a DIP mount, like shown in the photo.

Now that you know HOW BIG the prototype board will be, you can start thinking about how to box it.  Any electronics shop will give you many options if you search for ENCLOSURES.  Plastic is usually a better choice than metal for prototype enclosures because you don't have to worry about shorts.  The board will most often mount to the enclosure using STANDOFFS.

from wannatinker40.files.wordpress.com/2012/04/img_16621.jpg

Now, think about what the inputs and outputs are for your doohickey, including power, and think about how you're going to get those from the inside of the box to the outside of the box, and vice versa.  Choose connectors.  I like using 0.1" 2-row headers and ribbon cables to jump from the board to to box, so the board will be easily removable.  Choosing connectors will have to do with what's available, what steps you need to take to mount on your chassis (round holes are easiest), what's right for the job (e.g., 3.5mm jacks are bad for power because they short on insertion), etc.  Think about power.  Do you need to include a power supply, or can you use a wall wart converter and a barrel connector?  Make sure you include PROTECTION, like fuses. Think about any displays or other modes of output that you'd like.  LEDs are often convenient and easily mounted with the right hardware (see pic).  Think about your on/off switch and anything else you need in or on your box.  Picture your user actually using it, and use this exercise to find your omissions.


from hiviz.com/kits/images/components/LED_mount_med.jpg 

Lastly, now that you've done all this and have a parts list all ready to order, take that last moment and make sure your box is still big enough when you consider all the connectors and such. Think in 3D.  Your parts have height in addition to length and width.  make sure your enclosure is tall enough.

Then, place your order, machine your enclosure, and build your box. Make sure you LABEL all your I/O and controls.

 Here's one of my recent ones, built to NFPA99 specs for hospital safety, passed clinical engineering inspection, and (hopefully) soon to be deployed in an NICU.  I still need to add labels.  It uses a standard fused AC power entry module, and inside has a medical grade 5V power supply.  It uses a 5-pin DIN connector to bring in an external sensor.  There are illuminated buttons and paddle-type toggle switches.  The LED displays are home made I2C units, and required rectangular openings in the lid, which was a pain.