When you look in a dictionary, you will not find these derived words between the entries. You have to identify the root first, and then search for that root word. A good dictionary will explain the affixed forms too within the entry of the unaffixed form.  

The active prefix me- 
This prefix generally does not change the meaning of the root, but it emphasizes that a verb is being used in an active sense. 

The use of such active verbal prefixes is often optional. Even, this prefix me- can not be used with certain words. Pergi (= to go), for instance, can not be prefixed by me- become memergi which is meaningless. 

There are no certain rules, however,  to identify the words that can be prefixed by me-. The only way is to memorize them. 

This prefix me- is also used to create transitive verbs out of nouns and adjectives. In this case the root and the prefixed form have quite different, although related, meanings. 

merah = red  --> memerah = to turn red 
kunci = key  -->  mengunci = to lock 

Rules for prefixing me- 
You might be wondering about the result of prefixing me- in the above examples. Howcome me + kunci produces new word mengunci, rather than mekunci? And why me + tekan become menekan rather than metekan? 
You need to memorize the following rules to understand it. 

* me + s- ( words beginning with s-) produces meny- 
me + siram --> menyiram = to sprinkleme + sapu --> menyapu = to sweep, wipe off 

* me + words beginning with b- and p- produces mem- 
me + beli --> membeli = to buy 
me + bantu --> membantu = to help 
me + pukul --> memukul = to hit, strike 

* me + words beginning with k, g, h or any vowel produces meng- 
me + kunci   --> mengunci = to lock 
me + ganggu --> mengganggu = to bother, disturb 
me + hapus  --> menghapus = to erase 
me + ambil   --> mengambil = to take 

* me + words beginning with d, j, c and t produces men- 
me + dekat (adjective means near) -->  mendekat = to draw near 
me + jual  --> menjual = to sell 
me + cuci  --> mencuci = to wash 
me + tonton--> menonton = to watch (TV, movie or show) 

The first letters p, t, k, s of the root words are dropped when the prefix is added. One more example to make this clear : me + pakai --> memakai (=to use or to wear). 

The active prefix ber- 
The prefix ber- is used with Intransitive Verbs in almost the same way that me- is prefixed to transitive verbs. Prefixing with ber- here will create almost the same meaning words as the root, therefore this prefix is often omitted in everyday conversation. 

asal --> berasal = to originate 
bicara --> berbicara = to speak 
diri  --> berdiri = to stand 
kunjung  --> berkunjung = to pay a visit 

If this prefix is applied to an adjective or noun, ber- create an intransitive verb that has the meaning "possessing" or "taking the attribute of" the noun or adjective. 
kembang (= flower) --> berkembang = to blossom, expand, grow 
bahasa (=language)  --> berbahasa = to know or speak a language 
pakaian (=clothing)  --> berpakaian = to get dressed 
kata (=word)   --> berkata = to speak 

When prefixing words beginning with r, ber- becomes be-. So there is only one r appears in the result of  that prefixing. 
renang  --> berenang (not berrenang) = to swim 
rencana --> berencana = to plan 

The prefix ter- 
The prefix ter- is used to create superlative form (meaning "the most") when it is combined with adjectives. 
besar = big  -->  terbesar = the biggest 
indah = beautiful  -->  terindah = the most beautiful 

Another superlative form will be discussed later in Comparative section. 

When prefixing verbs or nouns, this prefix is used to indicate that an action has already been completed. With verbs, this prefix also creates a varian of passive form. 

atur = to arrange --> teratur = to be well organized, to be in order 
pakai = to use --> terpakai = to have been used 
kunci = key  --> terkunci = to be locked 

Kamarnya sudah terkunci = the room is already locked. 

The active prefix memper- 
The prefix memper- is used with adjectives to form transitive verbs. 

kuat = strong  -->  memperkuat = to strengthen 
besar = big  -->  memperbesar = to make bigger, enlarge 
panjang = long  -->  memperpanjang = to extend 

The above examples are active forms. The passive forms can be created by replacing the prefix mem- with di-, so the prefix becomes diper-. 
    memperbesar = to enlarge  -->  diperbesar = to be enlarged. 
 

* pe + word beginning with s- creates peny- 
   sakit = sick  --> penyakit = illness, disease 

* pe + word beginning with b- and p- creates pem- 
   beli = to buy  -->  pembeli = buyer 
   pakai = to use  -->  pemakai = user 

* pe + word beginning with c-, d-, j-, t- creates pen- 
   dengar = to hear  -->  pendengar = listener 
   jual = to sell  -->  penjual = seller 
   curi = to steal  -->  pencuri = thief 
   tonton = to watch  -->  penonton = viewer, spectator 

* pe + word beginning with g-, k- or any vowel creates peng- 
   ganti = to replace --> pengganti = one who replace, replacement 
   kejar = to chase  --> pengejar = chaser 
   urus = to take care of --> pengurus = person in charge 

The suffix -kan 
The suffix -kan, together with prefix me-, added to intransitive verbs, nouns and adjectives to form transitive verbs. While adding this suffix alone to intransitive verbs, nouns and adjectives creates imperative or request.  

   masuk = to enter, come in  --> masukkan = to put into 
   selesai = to be finished  -->  selesaikan = make it done 
   Selesaikan ini dalam dua hari = Finish it in two days. 

Imperatives will be discuss later in separate section. 

With prefix me-, this suffix can be used together to form an active transitive verb.  
   memasukkan (me + masuk + kan) = to put into 
   menyelesaikan = to finish 
   Saya belum menyelesaikan pekerjaan itu = I haven't finished that work yet. 
 
The suffix i- 
The suffix i- is added to intransitive verbs or adjectives to create transitive verbs which imply that something is being done by the subject. 
   datang = to come  -->  datangi = to pay a visit to 
   pinjam = to borrow  -->  pinjami = to lend 
   dekat = close, near  -->  dekati = to approach 
   Tolong pinjami saya uang = Please lend me some money 

The suffix -an 
The suffix -an is added to verbs to create nouns. 
   makan = to eat  -->  makanan = food 
   minum = to drink  -->  minuman = a drink 
   pinjam = to borrow  -->  pinjaman = loan, borrowings 
   kenal = to know  --> kenalan = acquintance 

The affix ke- + verbs/adjectives + -an 
This affix is added to verbs and adjectives to produce abstract nouns. 
   indah = beautiful  --> keindahan = beauty 
   aman = secure, safe  --> keamanan = security 
   baik = good, well  --> kebaikan = goodness 
   besar = big, large  --> kebesaran = greatness 

Kebesaran also means "too big" (adjective). This is one of inconsistencies in Indonesian. 
   Sepatu saya kebesaran = My shoes are too big. 

Note that the result of affixing with ber-, per-, -kan and -i are irregular and idiomatic. These prefixes cannot be applied to every verb, noun or adjective. As I've told you earlier that there are no certain rules in prefixing, it is suggested that you are better learn the resulting verbs (with the prefixes) as separate vocabulary items.