We will have the opportunity to spend almost 3 days and 2 nights in Prague wşth my wife in the beginning of April. So, I would like to learn whta things we should be focusing on in this limited duration. Any tips for sightseeing, nice but central hotels restaurants, cafes, lovely architecture would really be appreciated.

You have picked a fine time of year to visit this exiting city. Could you give us some idea of the kind of things that you like to do, hotel budget and expectations, etc? The lovely architecture is the easy part - you will be surrounded by it, particularly in the central part of the city.

http://www.prague.net/itineraries-in-prague
the link will give you an idea of some intinaries ,you can adjust them to suit yourself.
Prague is a fairly compact city as far as the tourist is concerned and sights easy enough to walk aroud,there is a very good public transport system that will get you to place quite easily also.
There are links to it as well as lots of other tourist info for you to look at.
Where are you staying so i can maybe suggest a few eating places nearby.

Thank you very much for the replies. My intention is to stay in a central hotel, which will have easy reach within city. As it will be a special weekend for us I will prefer an special place stay in the city center near to Charles Bridge or Wenceslas Square. Any tips would reaaly be a great favour for me. Thanks in advance.

I would not stay near Wenceslas Square.

Here is a nice, inexpensive, hotel - midway between the Old Town Square and the Charles Bridge - you can't get a better location:

http://www.7angels.cz/

For a most central location, consider the Hotel Metamorphis. It is located in the small square just behind the Tyn Church which is at one end of the main square, so you are just a few steps from the center but in a quieter location. It's a very nice hotel in an historic building - I would call it "special."

My favorite location for a hotel in Prague though is on Kampa Island, the island that is directly under the Charles Bridge. On Kampa Island I have stayed at the Kampa Gardens hotel which I would classify as upscale budget. Very nice clean rooms with furnishings that are towards Ikea in style, some with spectacular views but a few with no views at all so if staying there, ask. The rooms in front either have views of Old Prague across the river or a wall. Rooms in the back look out on the park and stream. Breakfast there is average. Kampa Island is a very peaceful oasis in the midst of the Prague crowds yet there is easy and direct access from the Island onto the bridge. The island has a nice park with fabulous views, particularly at night, of Old town Prague across the river. The main historic square is a ten minute walk at most from the Charles Bridge. The boat tours leave from Kampa Island.

Two of our favorite restaurants in Prague are the Mucha Restaurant about a block and a half off the square and Kampa 15 (or is it 14) on Kampa Island. Among the other Restuarants on Kampa Island is the Kampa Park that is quite upscale.

We quite enjoyed our stay at the Hotel Josef.
http://www.hoteljosef.com/
It was central but on a quiet side street. It's a very modern hotel, so it depends if that is what you are looking for, but we thought the rates were fantastic, especially compared to what we would pay for a similar hotel in other great European cities.
cheers,
CC

Second vote for the Hotel Metamorphis. I stayed in an apartment there for a week and really enjoyed it. The pictures on the website are a bit outdated, e.g., they have flat screen TVs now. Check out the reviews and pictures at tripadvisor.
http://www.hotelmetamorphis.cz/
http://goo.gl/Ph73G

A lot of people also recommend the Hotel Paris. I haven't stayed there, but plan to on my next visit.
http://www.hotel-paris.cz/
http://goo.gl/da8o8

If you want to be central, I suggest staying in or near Old Town. I agree with Bardo--would not choose Wenceslas Square. IMO it looked kind of seedy--not a place I would choose for a special weekend.

As walkabout and Bardo say, there are a lot better places to stay than Wenceslas Square.

Any recommendations for cafes or restaurants in Prague which will affect us in terms of the ambiance and taste?

http://www.cafelouvre.cz/en/
this is a stunning cafe ,not the cheapest place about but worth it for the experience.
Cafe Slavic gets a good name but I have never tried it.
The Municiple house,has several cafes and bars and the main cafe/bar sometimes has live music on at weekends,again not the cheapest of places but just a lovely place to visit.
http://www.obecni-dum.cz/web/en/homepage
you can do a tour of the building if you wish and if you have time to spare or the weather is particularly bad then it is a fall back suggestion.

One of my favourite places to eat in Prague is U Medvidku.
http://www.umedvidku.cz/index.php?op...mid=81&lang=en
traditional Czech food at pretty reasonable prices,the beer there is also pretty good and if you go through the back and up the stairs they have their own micro brewery there,well worth seeking out.It is pretty central and is close to the Narodni Trida metro/tram interchange.
The Kolkovna group of resturants get a very good name i have only ever been in the Olympia but thought it great.
the Klasterin Pivovar is another great favourite of mine mainly because they make their own beer but the food is very good,not the cheapest place in town but the beer and the food make it worthwhile visiting.
http://www.klasterni-pivovar.cz/en/
sorry I am no expert on finer dining in Prague as wnem I am there I am there for the Beer and tend to eat in the Hospodas,that's bars that serve food of which there are a great many in the city and worth going into for good local food and great beer at very good prices

Bellavista has both great ambiance and great tasting food.

Bellavista is right next to the Strahov monastery/brewery - a "must see" (especially the famous library). I suggest you go for the views even if you don't dine there. An afternoon coffee, tea, or dessert at an outdoor table during non-dining hours (2:00-5:00pm) is a great way to enjoy the best views of Prague without spending much money.

I would also plan on a beer at the monastery next door - very good stuff.

http://www.best-restaurants-prague.c...sta-prague.php

http://www.strahovskyklaster.cz/webm...me.asp?idk=257

http://www.klasterni-pivovar.cz/en/

Further to Bardo's post,the Libary has just been fully reopened after a massive refurbishment.I was in there during the later work and it was looking stunning even through the scaffolding etc.,well worth seeing.Of course a beer in the Klasterini Pivovar afterwards would not be a bad idea.