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For instructions on making the store itself, see Florist.  For a bookstore you will need a number of shelves, about 1/8 inch apart, and perhaps a few angled racks with books or magazines placed with the front covers facing the customer.  The counter should be small, at one side or in the middle.

I made the shelves for this shop out of folded heavy paper.  I cut a piece the width of the matchbox, then folded the paper horizontally so that it formed shelves and the wall behind them (see illustrations).  Then I cut more paper to trim top and bottom and to separate the four sections.

Materials required: Same as for the Florist shop.  In addition, you'll need some colour pictures from cards or magazine--anything with a good variety of colours will do.  Also useful: tiny pictures, perhaps cut from bigger ones, and tiny posters advertising  books.  Although you are presumably reading this on a computer, I'll assume you don't have a colour printer or scanner.  If you do, you'll be able to make book covers yourself.

For books lined up on the shelves with just their spines showing, cut strips of paper about 2 inches long and of uneven widths up to 1/8 inch wide, from a coloured picture.  Cut so that you have a number of colours on your strip.  Then fold it up like a concertina, and glue the concertina on a shelf so that the folds look like the spines of books. 

You can use plain colours for a set of matching books, or striped paper to suggest words on the spine. Except where you are making a matching set, vary the height of the books,

It will take a while to get the knack of glueing each concertina in place without having all the others jump out, but use plenty of glue and take your time. If you have used paper shelves, make sure that as you glue the books in place you keep the shelves straight.  The books should strengthen the structure.

You can fill some spaces with books with their covers facing out.  Choose pieces of paper with a suitable design for the front cover:  a face, perhaps, or a flower or a mountain, and cut and fold the paper so it looks like a book cover.  You don't need any pages in this case.

There should be a few books with pages, though, perhaps on the counter.  If the book is to be left shut, you can cut tiny squares of paper and stick them together, add a cover and then trim the edges with a razor blade.  If you get really carried away, use the glued edge of a writing pad or notebook, and cut out tiny rectangles from it so they are glued together on one side.  Add a cover of folded paper.

For a children's book store, put a couple of cushions on the floor (made of folded fabric or paper glued at the edges; glue just one edge at a time, and hold the edge together tightly with a clip; stuff with a scrap of tissue if desired, trim).  Cut out pictures of well-known figures like Winnie the Pooh (check copyright rules first) and stick them on the walls.

For a comic book store, or used book store, make the books the appropriate height and perhaps use rather faded colours.  Put books everywhere you can, in piles on top of boxes, and so on.  Posters of comic characters will help explain what kind of store this is.

For an elegant and expensive bookstore, choose colours carefully: probably use either very dark or very pale combinations.  You can try making books out of very fine leather, but they do tend to look lumpy no matter how thin the leather is. Paper painted with acrylic paint might look more realistic.  Be careful adding gilding; there are a lot of gold paints and pens and foils available, even in the local convenience store sometimes, but it's hard to make lines thin enough.  Consider starting with a book cover of gold foil paper, and then painting it all over, scratching off the paint here and there to reveal the gold.  A few pictures of well-known literary faces, like Shakespeare, will help indicate the kind of shop this is.

New ideas will arise as you work on these projects, so feel free to experiment.  If you have a good printer, there's nothing to stop you printing out real books with words or pictures in them.  Nothing but common sense, some would say.
Special projects in 1/144 scale
These are intended for people who do not have easy access to miniature supplies
I  have tried to use only tools and materials that are likely to  be in most homes or that could be found in a small supermarket or hardware store. The projects aren't suitable for complete beginners, but anyone with some experience making miniatures should be able to cope.
Bookshop in a matchbox
Toys in Miniature: Frances Armstrong
Next to come  in the matchbox series: a toy shop.  Instructions for making some of the toys will be found here:
Tiny houses
Tiny toys