6 days itenary for first time visitors

First thing I would recommend is to get the Rick Steves "Europe through the backdoor" travel book and most of your questions are answered there. If you really want to go into detail buy the France & Switzerland books. I find having a car in Europe to more of a hassle than help and prefer trains and buses and metros to get around. I also, prefer the small hotels listed in the books instead of Air B&B or other apartments because of the time consuming check in and check out of the private apartments. Sounds like your going to have a great time!

Because you have so little time, you will not need a car (its not like you will be touring all of Switzerland). Pick two places you want to visit. Train there from Paris. Pick places that are outdoorsy . Then make a b-line for Amsterdam

As for apartments or hotels, it depends what you prefer and what your budget is. I find that apartments are cheaper, but b&b's offer breakfast which is nice.

Jessica

Mahr,
It would be helpful if you would add this info: time of year, age of kids, interests (mountain tops? hiking, photog? etc), and budget constraints if any. Then future comments can zero in.
However, for now, here are some comments:
1. I've been to Switz. a dozen times and lived there too. Drove twice but used trains the next 10 times. I MUCH prefer trains. They are on time, get you everywhere, and no parking problems. Budget constraints might lead towards a car, however kids are generally free under 16 for trains and cable cars (look up "Family Card"). All routes and prices are on SBB.ch/en .

1. Private apt. will probably save you money, espec. if it has a kitchen that you use. Eating out in Switz. can get expensive. Start looking now on booking.com or vrbo.com or Airbnb.com because they are filling up .

2. The big cities aren't that interesting. With my kids we headed straight for the Alps. That means Lucerne, Lauterbrunnen, Grindelwald, Murren, or Engelberg. My one big city exception might be Geneva, since I lived there, and it is on the way from Paris to the alps. In Geneva, your family can rent bikes for free (geneveroule.ch), climb the bell tower at John Calvin's church, get free bus tickets if you stay overnight, walk within 10 feet of the giant water jet in the lake, etc.

3. If i read you right, you want nature outside the big cities, and the
   hikes in the Jungfrau/Berner Oberland region are just that. Cows,
   goats, farmers, trails, and huge mountains and valleys all around.
   Click on my name to see my previous posts on 10 great hikes in the
   area. See Rick Steves TV show on the alps to get a feel for the region.
   https://www.ricksteves.com/watch-read-listen/video/tv-show/best-of-the-alps

4. You can sometimes get a discount on some routes if you book in advance, BUT if you miss that time or your plans change, your ticket is voided. I've never found a train too full, and 95% of the time I get the ticket the same day. The one exception to that rule is that you MUST reserve the Paris to Geneva bullet train, in advance. The earlier the better for a discount fare.
   You could also consider the Swiss Pass or Berner Oberland Pass, and Rick writes about that on his website and in his books.

5. For Paris to Switzerland, I highly recommend the bullet train which travels close to 200 mph (what kid wouldn't like that?) and gets you to Geneva in 3 hours. It leaves Paris from Gare de Lyon and you must reserve in advance. Lots of info here, and take that authors advice and use trainline.eu and NOT RailEurope.com:

https://www.seat61.com/Europe-train-travel.htm

https://www.seat61.com/lyria.htm

You can then either stay a bit in Geneva or keep moving by train to Lauterbrunnen or nearby alps cities, and that is about another 3.5 hours, but a LOT nicer than car travel. Smooth and relatively quiet. The train office in Geneva is superb and will help book you thru to your final destination.

Paris - Switzerland - Amsterdam is a strange route. It is V-shaped. It would be more logical to do Amsterdam - Paris - Switzerland (or vice-versa), flying into Amsterdam and out of Zürich.
Amsterdam - Paris and Paris - Switzerland are a good distance for trains, and both routes have High Speed trains. If you decide on your original order, Switzerland - Amsterdam is a lot further and best done by air.
No way you want to do this by car. A car is a liability in Amsterdam or Paris, and not needed in Switzerland. High Speed trains take half the time it does to drive, and are a lot more comfortable. And one-way international car hire usually has a large surcharge.

There are two train routes from Paris to Switzerland:
(1) Paris - Geneva/Lausanne
(2) Paris - Basel - Zürich
Depending on where you are going in Switzerland one or the other route may be better.
The timetable for both routes is here: https://www.tgv-lyria.com/sites/default/files/pdf/BROCHURES_CO/lyria-timetable-10.12.17_06.07.18.pdf
Info page about the route here: https://www.seat61.com/lyria.htm
And watch the video here: https://www.youtube.com/watch?v=KrXUqOPU9wc

3- we are more interested to enjoy the nature than the city, so how we should plan our stay on each cities ? ( in Switzerland )

DO NOT stay in a city in Switzerland. Switzerland is about mountains and countryside, not cities.
The two normal locations for first time visitors are:
Jungfrau region (Lauterbrunnen, Grindelwald, Mürren or Wengen). Smaller locations half way up mountains. Website: https://jungfrauregion.swiss/en/summer/
Luzern Town with nice old town, lake (boat trips). 360° panorama: http://tour.luzern.com/360/en/
Both locations have mountains you can go up by train or cable car.

You need to decide which, and then come back and ask about train ticket options (this post is already getting too long). You need to buy High Speed train tickets 2-3 months in advance to get the cheap fares.

Ditto, If you can fly into Zurich, you can be in Luzern 2 to 3 hours after you walk out of the luggage collection room. Then it is a 2 hour scenic train ride to Interlaken Ost, then another hour connecting to those iconic Berner Oberland villages by train and maybe a cable car. On to Paris, about 5 hours from Interlaken Ost with a single change in Basel. Then to Amsterdam. Basel to Paris and Paris to Amsterdam are the only ones that should be bought in advance to get a discount for nonrefundable tickets.

To avoid future sticker-shock, be aware that the default rail fares for Swiss trains displayed on the SBB website assume that the purchaser holds the half-fare card. You need to double those fares to see what you would pay without having that discount card, which I think costs something like CHF 120 per adult.

Thank you all, very well contributed and helped me in my decision. The two major take away from your responses are :
1- avoid rent a car since it is a short trip
2- change in the country wide direction , my plan would be Amsterdam > Paris > Switzerland.
Thanks to Chris for this suggestion.

One important thing which I missed here to ask is , if I want to spit my stay in Switzerland into multiple places ( maximum 3 cities ), what should be those and the things to do nearby.

Once again thanks for helping us, the world is so close and small!!.

With 6 days, limit it to two locations in Switzerland. The aforementioned Berner Oberland is a good starting place coming from Paris. Then move on to Luzern, where you can get an early morning train direct to Zurich Airport for the flight home. Only a 1 hour journey. Whether you split it 4&2 or 3&3 is the question. I'd tend go with 4&2 as there are a lot of things to do in the Berner Oberland, hiking primarily, as easy or as strenuous as you care.

The 3 main towns would be Wengen, Muerren, and Lauterbrunnen. Lauterbrunen is in the valley between the other two. I always recommend stay on the mountain in one of the traffic-free villages. Of the two, Muerren has the postcard charm that spells Switzerland to most people.

I actually liked it better the other way up. According to your other post this will be at the end of March?

I assume you like flowers, especially tulips and hyacinths? The Keukenhof https://keukenhof.nl/en/ opens on the 23rd of March, and the later in March the better.

I'd wind up in Amsterdam.

You're aware with the snow not many of the higher trails at the Berner Oberland will be open?

Missed that on your other thread. It will still be ski season in the Berner Oberland in late March. There are still some winter walks, but sledding as well, and of course skiing. If you don't want to bring items like snow pants and snow boots, the shops will happily rent them to you. Bring parka like coats, and they may also come in handy in Paris and Amsterdam that time of year. Lodging in Muerren or Wengen may be at a premium, but it is getting to the end of the season. The winter school breaks will be over by then, so you could find a deal.

Edit - Buy those train tickets to Paris and Switzerland now while there are still some discount tickets available. How old are the kids? There me be discounts on top of that for them.

Edit - I see now from your other thread the kids are 5 and 8, 5 yo will travel with you for free in Switzerland. They will need some form of ID (birth dates listed on your passport?) to show their age.